2011 BRAIN MIND and BLUE BRAIN Annual Report

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 Luthi-Carter Lab . ................................................................................................................42 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

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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

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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

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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.

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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.

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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

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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

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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

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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.

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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

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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)

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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.

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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

© Copyright 2004-2012 EPFL for all material published in this report info.sv@epfl.ch 17

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

© Copyright 2004-2012 EPFL for all material published in this report info.sv@epfl.ch 18

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

© Copyright 2004-2012 EPFL for all material published in this report info.sv@epfl.ch 19

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.

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

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.

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.

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..).

Selected Publications

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.

© Copyright 2004-2012 EPFL for all material published in this report info.sv@epfl.ch 20

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.

© Copyright 2004-2012 EPFL for all material published in this report info.sv@epfl.ch 21

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

© Copyright 2004-2012 EPFL for all material published in this report info.sv@epfl.ch 22

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.

© Copyright 2004-2012 EPFL for all material published in this report info.sv@epfl.ch 23

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

© Copyright 2004-2012 EPFL for all material published in this report info.sv@epfl.ch 24

EPFL School of Life Sciences - 2011 Annual Report

BMI - Brain Mind Institute The mission of the Brain Mind Institute (BMI) is to understand the fundamental principles of brain function in health and disease, by using and developing unique experimental, theoretical, technological and computational approaches. The scientific challenge addressed by the BMI consists of connecting different levels of analysis of brain activity, such that cognitive functions can be understood as a manifestation of specific brain processes; specific brain processes as emerging from the collective activity of thousands of cells and synapses; synaptic and neuronal activity in turn as emerging properties of the biophysical and molecular mechanisms of cellular compartments.

Understanding information processing in the brain and its higher emerging properties is arguably one of the major challenges in the life sciences. Research at the BMI focuses on three main areas: i) Molecular neurobiology and mechanisms of neurodegeneration ii) Molecular and cellular mechanisms of synapse and microcircuit function up to the behavioural level and including metabolic aspects; iii) Sensory perception and cognition in humans. In all areas, the BMI strives to integrate knowledge gained by multidisciplinary approaches and across different disciplines and research laboratories. Finally, underlying all levels of analysis, research at BMI is characterized by a sustained interest in pathological processes.

In order to achieve these scientific goals, the Brain Mind Institute benefits from a unique academic environment: • An institute organized as a network of independent laboratories reflecting complementary technological approaches; each laboratory collaborates with several others within the institute in addition to cross-disciplinary interactions on campus.

• A campus that stands out as a premier technological university in engineering, computer science and basic sciences.

• An intimate collaboration with the Blue Brain Project which stands out as one of the most challenging neuroscience simulation and data basing projects worldwide.

• A proximity to and joint affiliations of our faculty with top university hospitals in Lausanne and Geneva in particular for projects related to cognition and neurodegenerative diseases.

• A new initiative in neuroprosthetics to which the BMI is strongly committed that will further the collaboration with engineering sciences by a host of inspiring common projects.

BMI - Brain Mind Institute

A feature of the Brain Mind Institute is that several faculty members have strong expertise in physics or mathematics; this holds not only for theoretical but also for experimental neuroscience. In this way, the Brain Mind Institute reflects the mission of the School of Life Science: to provide a life science curriculum with a strong emphasis on quantitative approaches. As far as teaching is concerned, the BMI Faculty is committed to provide a comprehensive and formal training in neuroscience from the undergraduate to the graduate levels. http://bmi.epfl.ch

© Copyright 2004-2012 EPFL for all material published in this report info.sv@epfl.ch 27

EPFL School of Life Sciences - 2011 Annual Report

Aebischer Lab http://len.epfl.ch

BMI

Patrick Aebischer was trained as an MD (1980) and a Neuroscientist (1983) at the University of Geneva and Fribourg in Switzerland.

From 1984 to 1992, he worked as a Faculty member at Brown University in Providence (USA). In 1991, he became the chairman of the Section of Artificial Organs, Biomaterials and Cellular Technology of the Division of Biology and Medicine of Brown University. In the fall of 1992, he returned to Switzerland as a Professor and Director of the Surgical Research Division and Gene Therapy Center at the Centre Hospitalier Universitaire Vaudois in Lausanne. In 1999, Patrick Aebischer was nominated President of EPFL by the Swiss Federal Council. He took office on March 17th, 2000. He is the founder of 3 biotech companies.

Patrick Aebischer Full Professor President of EPFL

Introduction

Our laboratory is involved in understanding the cause of neurodegenerative diseases of the central nervous system (CNS) and design effective treatments to slow down the progression of neuronal degeneration. We develop new technologies for animal modelling of the disease and comprehensive analysis of the degenerative process, and investigate therapies based on genes and compounds.

Recently developed viral vectors show unprecedented efficacy to deliver genetic information to the CNS and correct the molecular defects leading to devastating conditions such as fatal neuromuscular diseases. In addition, viral vectors can be used to introduce pathogenic genes in adult neurons and thereby generate rodent models to decipher the molecular mechanisms leading to complex brain disorders such as Parkinson’s and Alzheimer’s diseases.

Keywords

Gene therapy, animal models of disease, Parkinson’s disease, Amyotrophic lateral sclerosis, Alzheimer’s disease, viral vectors, adeno-associated virus, cell encapsulation, brain imaging.

Results Obtained in 2011

Adeno-associated viral vectors (AAV) have a remarkable capacity to broadly diffuse in the CNS and transfer genes to non-dividing cells, such as neurons and astrocytes. Based on this technology, our lab develops therapies against neuromuscular disorders such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). Harnessing the ability of AAV vectors to distally target neurons via axonal processes, we have generated specific vectors and explored routes of administration to transduce motor neurons across the entire spinal cord. In particular, we have used this approach to deliver miRNA-based silencing instructions against mutated human SOD1, a protein involved in familial forms of ALS. Specific vectors were generated to lower SOD1 levels in both neurons and astrocytes, two cell types crucially implicated in ALS pathogenesis. We are currently assessing the neuroprotective effect of this gene therapy approach in the G93ASOD1 mouse model for ALS.

For Alzheimer’s disease, we used AAV vectors to express the amyloid precursor (APP) and tau genes in the mouse brain and develop rodent models of the pathology that show accumulations of the pathogenic proteins and degenerative effects. In collaboration with the Paul Scherrer Institute at Villigen, our laboratory was involved in developing novel imaging approaches to assess amyloid plaque pathology, an histopathological signature of Alzheimer’s disease. Quantitative assessment of amyloid pathology in the mouse brain was achieved using coherent X-ray tomography.

In the frame of Parkinson’s disease, the animal model based on AAV-mediated overexpression of human α synuclein previously established in our laboratory was used to explore particular aspects of the on going pathology. We found that α-synuclein accumulation leads to deficient dopamine neurotransmission in the striatum, preceding overt neurodegeneration. Defects in dopamine neurotransmission contribute to the apparition of motor symptoms in these animals. In addition, these functional defects are linked to impairments in the secretory pathway of the diseased neurons. We are currently exploring these aspects of the AAV α-synuclein model to design symptomatic and neuroprotective treatments that may better address the pathological features observed in these animals. In addition, adenoviral vectors for the expression of the G2019S mutated form of LRRK2 in dopaminergic neurons of the substantia nigra recapitulate neurodegenerative features consistent with the prevalent forms of LRRK2-associated Parkinson’s disease.

We are currently exploring innovative therapeutic approaches that aim at preventing neuronal degeneration. In this context, we develop bioactive cellular implants for the chronic delivery of recombinant antibodies. This approach may find application for passive immunization against the pathogenic proteins implicated in neurodegenerative disorders.

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EPFL School of Life Sciences - 2011 Annual Report

Aebischer P. Philanthropy: The price of charity, Nature, 481:260, 2012.

Ciron C., Lengacher S., Dusonchet J., Aebischer P., Schneider B.L., Sustained expression of PGC-1α in the rat nigrostriatal system selectively impairs dopaminergic function, Hum Mol Genet., 21:1861-76, 2012.

P.G. Coune, J.C. Bensadoun, P. Aebischer, B.L. Schneider, Rab1A Over-Expression Prevents Golgi Apparatus Fragmentation and Partially Corrects Motor Deficits in an Alpha-Synuclein Based Rat Model of Parkinson’s Disease, Journal Parkinsons Dis., 1:373-387, 2011.

O. Marroquin Belaunzaran, C. Campana, M. I. Cordero, V. Setola, S. Bianchi, C. Galli, N. Bouche, V. Mlynarik, R. Gruetter, C. Sandi, J.-C. Bensadoun, M. Molinari, P. Aebischer, Chronic Delivery of Antibody Fragments Using Immunoisolated Cell Implants as a Passive Vaccination Tool, Plos One, 6:e18268, 2011 .

K. Löw, P. Aebischer, Use of viral vectors to create animal models for Parkinson’s disease, Neurobiol. Dis., 2011.

J. Dusonchet, O. Kochubey, K. Stafa, S.M. Young Jr., R. Zufferey, D.J. Moore, B.L. Schneider, P. Aebischer, A rat model of progressive nigral neurodegeneration induced by the Parkinson’s disease-associated G2019S mutation in LRRK2, J Neurosci, 31:907-12, 2011.

C. Towne, V. Setola, B.L. Schneider, P. Aebischer, Neuroprotection by Gene Therapy Targeting Mutant SOD1 in Individual Pools of Motor Neurons Does not Translate into Therapeutic Benefit in fALS Mice, Mol Ther, 19:274-83, 2011.

Neurodegenerative Disorders: Gene Therapy on Clinical Trial, P. Aebischer.

Frontiers in Neuroscience, vol. 4, p. 138-139, 2010.

C. Towne, B.L. Schneider, D. Kieran, DE Redmond Jr, P. Aebischer, Efficient transduction of non-human primate motor neurons after intramuscular delivery of recombinant AAV serotype 6, Gene Ther, 17:141-6, 2010.

K. Langou, A. Moumen, C. Pellegrino, J. Aebischer, I. Medina, P. Aebischer, C. Raoul, AAV-mediated expression of wild-type and ALS-linked mutant VAPB selectively triggers death of motoneurons through a Ca2+-dependent ER-associated pathway, J Neurochem, 114:795-809, 2010.

Team Members Research Associates Bernard Schneider

Postdoctoral Fellows Julianne Aebischer Matthias Cacquevel Carine Ciron David Genoux Karin Löw Veronica Setola PhD students Philippe Coune Wojciech Bobela Elisabeth Dirren Aurélien Lathuilière Emilda Pino Lu Zheng Master’s students Marc Godbille Dominique Rubi Technicians Aline Aebi Philippe Colin Fabienne Pidoux Vivianne Padrun Christel Sadeghi Delphine Ernst (visiting) Marc-Antoine Perrenoud (visiting) Jonas Carrel (visiting Visiting Students Pamela Valdes Katherine Li (SRP) Maria Zamfir Administrative Assistant: Ursula Alves-Zwahlen

BMI - Brain Mind Institute

Selected publications

(A) Histology of an amyloid plaque generated in the mouse hippocampus by injection of an AAV vector encoding mutated human APP. Three-dimensional plaque imaging by coherent X-ray tomography in the 5xFAD Alzheimer’s mouse model: X-ray plaque imaging (B) is compared with the classical thioflavin S histology (C). D shows cortical amyloid deposition. Figure adapted from: Imaging brain amyloid deposition using grating-based differential phase contrast tomography. Pinzer BR, Cacquevel M, Modregger P, McDonald SA, Bensadoun JC, Thuering T, Aebischer P, Stampanoni M. Neuroimage. 2012

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EPFL School of Life Sciences - 2011 Annual Report

Blanke Lab http://lnco.epfl.ch

Olaf Blanke

BMI

Olaf Blanke is director of the Center for Neuroprosthetics at the Ecole Polytechnique Fédérale de Lausanne (EPFL), holds the Bertarelli Foundation Chair in Cognitive Neuroprosthetics, and is consultant neurologist at the Department of Neurology (Geneva University Hospital). He received his MD and PhD in neurophysiology from the Free University of Berlin. Blanke’s research targets the brain mechanisms of body perception, corporeal awareness and self-consciousness, applying paradigms from cognitive science, neuroscience, neuroimaging, robotics, and virtual reality in healthy subjects and neurological patients. His two main goals are to understand and control neural own body representations to develop a neurobiological model of self-consciousness and to apply these findings in the emerging field of cognitive and systems neuroprosthetics.

Associate Professor

Introduction

The Laboratory of Cognitive Neuroscience targets the functional and neural mechanisms of body perception, corporeal awareness and self-consciousness. Projects rely on the investigation of healthy subjects and neurological patients by combining psychophysical and cognitive paradigms with state of the art neuroimaging techniques such as intracranial EEG, surface EEG, and fMRI. Our interdisciplinary expertise – bridging neurology, epileptology, intracranial electrophysiology, cognitive science, and neuroimaging – also includes engineering-based approaches to cognitive science: a virtual reality (VR) neuroimaging platform with a portable high-density EEG system, a vestibular stimulation platform with an integrated high-density EEG system, and several haptic platforms for neuroscience robotics in conjunction with fMRI. Next to studying the brain mechanisms of body perception, cognition, and self-consciousness, we actively pursue our translational neurorehabilitation research and interdisciplinary fields of virtual reality, presence research, brain-computer interfaces.

Results Obtained in 2011

A major development and result in 2011 was the description of a novel robotic stimulation device that can be used jointly with non-invasive brain imaging in humans (3T magnetic resonance imaging). The device was built in collaboration with the Laboratory of Prof Roger Gassert (ETH Zurich) and allowed us to describe for the first time the brain mechanisms in temporo-parietal cortex related to key aspects of bodily self-consciousness (self-location; firstperson perspective) (Ionta et al., 2011). We have further developed the MRI-compatible robot (Duenas et al., 2011), which is currently involved in a number of ongoing behavioral and brain imaging projects.

Keywords

Multisensory integration, sensorimotor, neuroscience robotics, perception, neuroprosthetics, temporo-parietal cortex, bodily awareness, self-consciousness, self-location, first-person perspective, neuroimaging, fMRI, EEG, neuropsychology, cognitive neuroscience, neurology, virtual reality, vestibular system, mental imagery.

Brain region in temporo-parietal cortex reflecting robotically-controlled changes in self-location in healthy participants using fMRI (red region) and neurologically-induced changes in self-location in neurological patients (blue region).

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Arzy, S., Collette, S., Wissmeyer, M., Lazeyras, F., Kaplan, P. W., & Blanke, O. (2011). Psychogenic amnesia and self-identity: a multimodal functional investigation. European Journal of Neurology 18, 1422-1425.

Arzy, S., Mohr, C., Molnar-Szakacs, I., & Blanke, O. (2011). Schizotypal perceptual aberrations of time: correlation between score, behavior and brain activity.

PLoS One 6, e16154.

Dieguez, S., Scherer, J., & Blanke, O. (2011). My face through the lookingglass: The effect of mirror reversal on reflection size estimation. Consciousness & Cognition 20, 1452-1459.

Dueñas, J., Chapuis, C., Pfeiffer, C., Martuzzi, R., Ionta, S., Blanke, O., et al.

(2011). Neuroscience robotics to investigate multisensory integration and bodily awareness. Engineering in Medicine and Biology Society (EMBC) IEEE 8348-8352.

Hansel, A., Lenggenhager, B., von Kanel, R., Curatolo, M., & Blanke, O. (2011).

Seeing and identifying with a virtual body decreases pain perception. Eur J Pain 15, 874-879.

Ionta, S., Heydrich, L., Lenggenhager, B., Mouthon, M., Fornari, E., Chapuis, D., et al. (2011). Multisensory mechanisms in temporo-parietal cortex support self-location and first-person perspective. Neuron 70, 363-374.

Team Members Postdoctoral Fellows Kanayama Noriaki Llobera Mahy Joan Martuzzi Roberto Salomon Roy Prsa Mario Bolomey Léandre Garipelli Gangadhar Palluel Estelle Herbelin Bruno Ionta Silvio Van Elk Michiel

PhD students Berger Steve Michel Jimenez Rezende Danilo Pfeiffer Christian Kaliuzhna Mariia Pozeg Polona Marclay Samuel Monnard Guillaume Evans Nathaniel Gale Steven Administrative Assistant Gordana Kokorus

Lenggenhager, B., Halje, P., & Blanke, O. (2011). Alpha band oscillations correlate with illusory self-location induced by virtual reality. Eur J Neurosci, 33, 1935-1943.

Lopez, C., & Blanke, O. (2011). The thalamocortical vestibular system in animals and humans. Brain Res Rev. 67, 119-146.

Lopez, C., Mercier, M. R., Halje, P., & Blanke, O. (2011). Spatiotemporal dynamics of visual vertical judgments: early and late brain mechanisms as revealed by high-density electrical neuroimaging. Neuroscience 181, 134-149.

Palluel, E., Aspell, J. E., & Blanke, O. (2011). Leg muscle vibration modulates bodily self-consciousness: integration of proprioceptive, visual, and tactile signals. J Neurophysiol, 105(5), 2239-2247. van Elk, M., & Blanke, O. (2011a). Manipulable objects facilitate cross-modal integration in peripersonal space. PLoS One 6, e24641.

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van Elk, M., & Blanke, O. (2011b). The relation between body semantics and spatial body representations. Acta psychologica, 138, 347-358.

fMRI-compatible neuroscience robotics. The robotic device is placed in the MR scanner. The device’s structure with ultrasonic motors, linear guides and stroking spheres is shown.

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EPFL School of Life Sciences - 2011 Annual Report

Fraering Lab

http://fraering-lab.epfl.ch

Patrick Fraering

BMI

Patrick Fraering studied biology at the University Louis Pasteur of Strasbourg, where he earned a master’s degree in biochemistry (1995) and pre-doctoral research degree in molecular and cellular biology at the CNRS (1996). In 2001, he received his PhD, conducting biochemical studies on the GPI-transamidase complex and on the process of protein secretion at the University of Fribourg.

In 2002, he joined the lab of Prof. D. Selkoe at Harvard Medical School where he has been focusing on the structure and function relationships of γ-secretase, an intra-membrane-cleaving protease responsible for the production of the Alzheimer’s disease amyloid-β peptides. In 2007, he was appointed assistant professor at the EPFL’s School of Life Sciences.

Tenure Track Assistant Professor Merck-Sorono Chair in Neuroscience

Introduction

The Laboratory of Molecular and Cellular Biology of Alzheimer’s Disease has a clear focus on the biochemistry, pharmacology and neurobiology of γ-secretase, an intramembrane-cleaving protease that is directly implicated in the generation of the amyloid-beta peptides (Aβ), which are central players in the pathogenesis of Alzheimer’s disease (AD). Our long-term goals are i) To get new insight into the structure-function relationships of γ-secretase, ii) To shed new light on the neurobiological functions of γ-secretase, and iii) To develop new therapeutic strategies to selectively reduce Aβ production by modulating γ-secretase activity.

Keywords

Molecular & cellular biology of Alzheimer’s disease, γ-secretase, amyloid-beta peptides (Aβ), intramembranecleaving proteases, therapeutic targets.

Results Obtained in 2011

Mercury is a direct and potent γ-secretase inhibitor affecting Notch processing and embryonic development. Prenatal exposure to mercury causes neurodevelopmental and neurological pathologies in infants, such as microcephaly and mental retardation. Since γ-secretase and the Notch pathway regulate neuronal differentiation and survival during development, and since Notch receptor signaling relies on cleavage by γ-secretase, we investigated mercury effects on γ-secretase in vitro and in vivo. We found that mercury inhibits Notch processing in a γ-secretase cell-free assay and in embryos collected from adult Drosophila melanogaster treated with mercury. This was accompanied by severe neurodevelopmental abnormalities in embryos. Our findings provide first evidence that mercury is a direct and potent γ-secretase inhibitor and suggest that disruption of the Notch pathway contributes to mercury-induced toxicity in the nervous system.

Selective neutralization of APP-C99 with monoclonal antibodies reduces the production of Alzheimer’s Aβ peptides.

Recent phase 3 clinical trials testing γ-secretase inhibitors revealed unwanted side effects likely attributed to impaired

Notch cleavage, critically involved in cell fate regulation.

We developed a new therapeutic approach to reduce Aβ production with monoclonal antibodies selectively targeting the Amyloid-β Precursor Protein C-terminal fragment, without affecting other γ-secretase functions. These antibodies, generated by immunizing mice with recombinant human APP-C99 adopting a native conformation, bound accessible N- or C-terminal epitopes of this substrate and led to reduced Aβ levels in vitro and in vivo.

Processing of the synaptic cell-adhesion molecule neurexin3β by Alzheimer’s disease α- and γ-secretases. Neurexins (NRXNs) and Neuroligins (NLGNs) are synaptic cell adhesion molecules having essential roles in the assembly and maturation of synapses into fully functional units. We found that the α-secretase metalloprotease TACE/ADAM17 and γ-secretase can sequentially process neurexin-3β (NRXN3β), leading to the formation of two final products: a ~80 kDa N-terminal extracellular domain (sNRXN3β) and ~12 kDa C-terminal intracellular domain (NRXN3β-ICD), with both of them being potentially implicated in the regulation of NRXNs and NLGNs functions at the synapses. Importantly, we found that this processing is altered by several mutations in presenilin-1 (PS1, the catalytic subunit of the γ-secretase) that cause early-onset familial Alzheimer’s disease (FAD).

Alzheimer’s disease-linked mutations in Presenilin-1 result in a drastic loss of activity in purified γ-secretase complexes. Mutations linked to FAD are found most frequently in PSEN1, the gene encoding PS1. We took advantage of a mouse embryonic fibroblast cell line lacking PS1 and PS2 to purify human γ-secretase complexes with the pathogenic PS1 mutants L166P, ΔE9, or P436Q. The functional characterization of these complexes revealed that all PS1 FADlinked mutations caused a drastic reduction of Aβ and APP intracellular domain productions in vitro. Our findings support the view that PS1 mutations lead to a strong γ-secretase loss-of-function phenotype associated with an increased Aβ1-42/Aβ1-40 ratio, two mechanisms that are potentially involved in the pathogenesis of AD.

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

J. Houacine, T. Bolmont, L. Aeschbach, M. Oulad-Abdelghani, and PC. Fraering. (2012). Selective neutralization of APP-C99 with monoclonal antibodies reduce the production of Alzheimer’s Aβ peptides. Neurobiol Aging. 2012 Feb 6.

M. Cacquevel, L. Aeschbach, J. Houacine, and PC. Fraering. (2012). Alzheimer’s disease-linked mutations in Presenilin-1 result in a drastic loss of activity in purified γ-secretase complexes. Plos One, In press.

JR Alattia, T. Kuraishi, I. Chang, B. Lemaître, and PC. Fraering. (2011). Methylmercury is a direct and potent γ-secretase inhibitor affecting Notch processing and embryonic development. FASEB Jul;25(7):2287-95.

Bot N, Schweizer C, Ben Halima S, and Fraering PC. (2011). Processing of the synaptic cell-adhesion molecule neurexin-3b by Alzheimer’s disease α- and γ-secretases. J Biol Chem. Jan 28;286(4):2762-73.

F. Wu, C. Schweizer, N. Rudinskiy, DM. Taylor, A. Kazantsev, R. Luthi-Carter and PC. Fraering. (2010). Novel γ-secretase inhibitors uncover a common nucleotide-binding site in JAK3, SIRT2 and PS1. FASEB, Jul;24(7):2464-74.

Team Members Postdoctoral Fellows Jean-René Alattia Claude Schweizer Tristan Bolmont Nathalie Bot PhD students Jemila Houacine Mitko Dimitrov Isabelle, Magold Sebastien Mosser Magda Palcynska Master’s Student Andrzej Fligier Techician Lorene Aeschbach Administrative Assistant Caroline Rheiner

BMI - Brain Mind Institute

Model for the processing of APP-C99 by γ-secretase. Monoclonal antibodies targeting the substrate prevent its binding to the enzyme (I), and/or preclude its entrance in the cavity of the enzyme (II), and/or block the release of the Aβ product (III). Green star: substrate binding site; red star: catalytic site.

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EPFL School of Life Sciences - 2011 Annual Report

Gerstner Lab http://lcn1.epfl.ch

BMI

Wulfram Gerstner is Director of the Laboratory of Computational Neuroscience LCN at the EPFL. He studied physics at the universities of Tubingen and Munich and received a PhD from the Technical University of Munich. His research in computational neuroscience concentrates on models of spiking neurons and spike-timing dependent plasticity, on the problem of neuronal coding in single neurons and populations, as well as on the role of spatial representation for navigation of rat-like autonomous agents. He currently has a joint appointment at the School of Life Sciences and the School of Computer and Communications Sciences at the EPFL. He teaches courses for physicists, computer scientists, mathematicians, and life scientists.

Wulfram Gerstner

Full Professor Life Sciences and Computer & Communication Sciences

Introduction

The Laboratory of Computational Neuroscience uses theoretical methods from mathematics, computer science, and physics to understand brain function. Questions addressed are: what is the code used by neurons in the brain? How can changes of synapses lead to learning?

Keywords

Modeling, Hebbian learning, spike-timing dependent plasticity, simulation, spiking neuron models.

Results Obtained in 2011

We have been active in three different, but connected areas: Single-Neuron Modeling: We have shown that the electrical behaviour of neurons under somatic current or conductance injection can be well described by simplified neuron models with only one or two equations. The parameters of these neuron models can be directly extracted from experimental data. We found that the best simplified neuron model is an exponential integrate-and fire model combined with adaptation and/or refractoriness.

The work on single-neuron modeling involves collaborations with the labs of Henry Markram and Carl Petersen.

Modeling synaptic plasticity: We have developed a model that combines induction of synaptic plasticity with consolidation of synapses. The model of induction accounts for induction of Long-Term Potentiation under protocols of voltage-dependent and Spike-Timing Dependent Plasticity and leads to the tagging of the synapse. We studied consequences of plasticity in a recurrent network (Nature Neuroscience 2010).

We also studied the role of plasticity of inhibitory synapses and showed that a generic class of inhibitory learning rules leads to a stabilisation of network dynamics, since inhibition automatically balances excitation (Science 2011).

Network Simulation: In two collaborations with the labs of Michael Herzog and Carl Petersen, we simulate properties of networks of neurons. Christian Tomm, who works with data from the Petersen lab obtained interesting results on network topology which will be submitted in 2012.

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

T. Vogels, H. Sprekeler, F. Zenke, C. Clopath and W. Gerstner, (2011),Inhibitory Plasticity Balances Excitation and Inhibition in Sensory Pathways and Memory Networks, Science, Vol. 334, Nr. 6062, pp. 1569-1573.

R. Naud, F. Gerhard, S. Mensi and W. Gerstner, (2011),Improved Similarity Measures for Small Sets of Spike Trains, Neural Computation, Vol. 23, Nr. 12, pp. 3016-3069.

H. Markram, W. Gerstner and P.J. Sjöström, (2011), A history of spike-timingdependent plasticity, Frontiers in Synaptic Neuroscience, Vol. 3, Nr. 4, pp. 1-24.

F. Gerhard, R. Haslinger and G. Pipa, (2011), Applying the Multivariate TimeRescaling Theorem to Neural Population Models., Neural Computation, Vol. 23, Nr. 6, pp. 1452-1483.

F. Gerhard, G. Pipa, B. Lima, S. Neuenschwander and W. Gerstner, (2011), Extraction of network topology from multi-electrode recordings: Is there a smallworld effect?, Frontiers in Computational Neuroscience, Vol. 5, Nr. 4, pp. 1-13.

Hennequin, G., Gerstner, W., Pfister, J-P. (2010). STDP in adaptive neurons gives close-to-optimal information transmission Frontiers in computational neuroscience, 4(143).

Frémaux, N., Sprekeler, H., Gerstner, W. (2010). Functional Requirements for Reward-Modulated Spike-Timing-Dependent Plasticity. Journal of Neuroscience 30(40):13326-13337.

Team Members Postdoctoral Fellows Richard Naud Kerstin Preuschoff Tim Vogels

PhD students Mohammadjavad Faraji Nicolas Fremaux Felipe Gerhard Guillaume Hennequin Danilo Jimenez Rezende Skander Mensi Richard Naud Christian Pozzorini Alex Seeholzer Carlos Stein Christian Tomm Friedemann Zenke Lorric Ziegler Research Assistants William Podlaski Hesam Setareh Administrative Assistant Chantal Mellier

BMI - Brain Mind Institute

Clopath, C., Büsing, L., Vasilaki, E., Gerstner, W. (2010). Connectivity reflects coding: a model of voltage-based STDP with homeostasis. Nature Neuroscience, 13(3):344–35.

Hand movement simulated in a learning net of spiking neurons.

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EPFL School of Life Sciences - 2011 Annual Report

Hadjikhani Group http://sv.epfl.ch/faculty

BMI

Nouchine Hadjikhani completed her studies and her doctorate of medicine at the University of Lausanne. After a postdoc at the Karolinska Institute in Stockholm, she continued her career as a brain imaging research in Boston, at the Martinos Center for Biomedical Imaging, Massachusetts General Hospital, where she is now Associate Professor in Radiology at Harvard Medical School. Since 2006, she also has been holding a position as SNF Professor at the Brain Mind Institute at EPFL.

Nouchine Hadjikhani SNSF Professor

Introduction

The theme of our research is the neuroanatomical bases of emotional, social and cognitive difficulties in autism. Our lab is also interested in examining the pathophysiology and the possible role of the cerebellum in migraine.

Keywords

Functional and anatomical brain imaging, cognition, emotion, autism, plasticity, migraine, cerebellum.

Results Obtained in 2011

Our lab has been working at not only performing research on autism spectrum disorders, but also on informing the public about this condition, and organize meeting with parents’ associations to provide a better understanding of autism.

In collaboration with the team of Genetics at the CHUV and the Center for Integrative Genomics at UNIL, we were in 2010 the recipients of the Leenaards prize for Scientific research. The project awarded will study the phenotype, including behavioral, anatomical and functional profile, of a newly described copy number variant of the chromosome 16p11.2, strongly associated with autism and obesity. From this collaboration, a paper has already been pub-

lished in Nature describing for the first time an association between a genetical microdeletion and obesity. Our collaboration has also lead to the award of a Synergia grant, extending our research to an animal model.

Autism spectrum disorders (ASD) are characterized by difficulties in social interactions, and in emotion expression.

We are pursuing to understand of the neuroanatomical and functional bases of this disorder. Our data show that there is a delay in the maturation in the white matter connection in the brain of individuals with autism. We also demonstrated the impact to specifically cueing autistic individuals to look at the eyes in faces both for behavioral performance and for brain activation in areas involved in social cognition and emotion.

In parallel, we are pursuing, in collaboration with our group at the Harvard Medical School in Boston, our research on migraine, its physiopathology and its long-term effect on the brain.

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Granziera C, Daducci A, Meskaldji D, Roche A, Maeder P, Michel P, Hadjikhani N, Sorensen G, Frackowiak R, Thiran J.P., Meuli R, Krueger G. A new early and automated MRI-based predictor of motor improvement after stroke Neurology 2012; in press.

Van den Stock J, Vandenbulke M, Zh Qi, Hadjikhani N, de Gelder B. Developmental prosopagnosia in a patient with hypoplasia of the vermis cerebelli.

Neurology 2012, in press.

Van der Zwaag W, Da Costa S, Zurcher N.R, Adams R.B, Hadjikhani N. A 7 Tesla fMRI study of amygdala response to fearful faces. Brain Topogr. 2012; in press.

Donnelly N, Zurcher N, Cornes K, Snyder J, Naik P, Hadwin J, Hadjikhani N. Discriminating grotesque from typical faces: evidence from the Thatcher illusion. PLoS One. 2011;6(8):e23340.

Mainero C, Boshyan J, Hadjikhani N. Altered functional resting-state connectivity in the periacqueductal gray networks in migraine. Annals of Neurology.

2011;70(2):838-845.

Team Members Postdoctoral Fellows Cristina Granziera Loyse Hippolyte Ophélie Rogier PhD Student Nicole Zürcher Master’s Students Elvira Pirondini Lorenzo Casari Research Coordinator Karine Métrailler Scientific Collaborators Anthony Lissot Anne Maillard Torsten Ruest Administrative Assistant Carole Burget

Adams RB, Franklin RG, Kveraga K, Ambady N, Kleck RE, Whalen P, Hadjikhani N, Nelson AJ. Amygdala responses to averted vs direct gaze fear vary as a function of presentation speed. Soc Cogn Affect Neurosci 2011;Epub ahead of print. .

Granziera C, Hadjikhani N, et al. In vivo imaging of the structural core of Papez circuit in humans. NeuroReport. 2011;22(5):227-31.

Jacquemont S, et al. Epigenetic modification of the FMR1 gene in fragile X leads to a differential response to the mGluR5 antagonist AFQ056. Science Transl Med. 2011;3:64ra1.

Adams RB Jr, Franklin RG Jr, Rule NO, Freeman JB, Kveraga K, Hadjikhani N, Yoshikawa S, Ambady N. Culture, Gaze and the neural processing of fear expressions. Soc Cogn Affect Neurosci 2010 5(2-3) :340-8.

Hadjikhani N. Serotonin, pregnancy and increased autism prevalence: is there a link? Medical Hypotheses 2010;74(5):880-32.

BMI - Brain Mind Institute

Walters RG, Jacquemont S. et al., A novel highly-penetrant form of obesity due to microdeletions on chromosome 16p11.2, Nature 463, 2010, 671-675.

Perspectives on the brain

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EPFL School of Life Sciences - 2011 Annual Report

Herzog Lab http://lpsy.epfl.ch/

BMI

Michael Herzog studied Mathematics, Biology, and Philosophy. In 1996, he earned a PhD. in biology under the supervision of Prof.

Fahle (Tübingen) and Prof. Poggio (MIT). Then, he joined Prof.

Koch’s lab at Caltech as a post-doctoral fellow. From 1999-2004, Dr. Herzog was a senior researcher at the University of Bremen and then he held a professorship for neurobiopsychology at the University of Osnabrück for one year. Since 2004, Dr Herzog is a professor of psychophysics at the Brain Mind Institute at the EPFL where he has established his lab.

Michael Herzog Associate Professor

Introduction

In humans, vision is the most important sensory modality.

Surprisingly, the mechanisms of even the simplest forms of visual processing, such as spotting a pen on a cluttered desk, are largely unknown. For this reason, robots are still “object blind”. Our research aims to understand how and why humans can cope with visual tasks so remarkably well.

Keywords

Vision research, spatio-temporal vision, schizophrenia research, psychophysics, TMS, EEG, modelling.

Results Obtained in 2011

Vision is not retinotopic, i.e., we perceive the world in Euclidian coordinates independent of eye and head movements. When we turn our heads, the world remains stable even though the image of the world rotates on the retina.

To study how the information on our retinae is transformed into the Euclidian framework, we have developed a number of paradigms for non-retinotopic vision in the last years. Here, we used these paradigms to show that attention is processed retinotopically (Boi et al., 2011; Aydin et al., 2011b) and we characterized non-retinotopic feature integration in more detail.

The population of the developed world is aging faster than at any time before. In Europe, for example, the percentage of people of age 65 and older will increase from 17.4% in 2010 to 30.0% in 2060 (European Demography Report 2010, European Commission). Aging affects all kinds of

human functions even in the absence of age-related diseases such as Alzheimer’s and Parkinson’s. Age-related visual deficits occur on the level of the eye (optical deficits), the visual cortex (perceptual deficits), and in higher cortical areas (cognitive deficits). Whereas optical and cognitive deficits are widely studied, little is known about the effects of aging on perception. We have developed a test for visual aging which is little affected by optical deficits and is not related to cognitive and motor functions and potential deficits (Roinishvili et al., 2011).

With this paradigm and high density EEG recordings, we have shown that healthy elderly use very different brain areas to solve the visual task than younger controls (see figure below and Plomp et al., 2011). Healthy elderly (ELD) and younger controls (CON) performed a visual discrimination task in four conditions (vernier, long SOA, short SOA, mask only). We recorded high density EEG. On the left, global field power is shown in the four conditions for ELD and CON separately. Global field power (GFP) is an overall measure of brain activity. It is obvious, that brain activity of elderly is strongly diminished. For example, at 200ms after stimulus onset, a strong GFP peak occurs in the controls but not in the elderly. On the right, maps are shown that correspond to single electrode activity. Obviously, elderly show, particularly at around 200ms, clearly different maps than controls (compare maps 3 and 5). Our observations suggest that in most conditions, elderly use very different brain areas to solve the visual tasks than younger controls.

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Boi M, Vergeer M, Ögmen H, Herzog MH (2011) Nonretinotopic Exogenous Attention. Current Biology, 21(20), p1732-1737.

Plomp G, Kunchulia M, Herzog MH (2011) Age-related changes in visually evoked electrical brain activity. Hum Brain Mapp. doi: 10.1002/hbm.21273.

Roinishvili M, Chkonia E, Stroux A, Brand A, Herzog MH (2011) Combining vernier acuity and visual backward masking as a sensitive test for visual temporal deficits in aging research. Vision Research, 51(4), p417-423.

Boi M, Ögmen H, Herzog MH (2011) Motion and tilt aftereffects occur largely in retinal, not in object, coordinates in the Ternus-Pikler display. Journal of Vision, 11(3):7, p1-11.

Sayim B, Westheimer G, Herzog MH (2011) Quantifying target conspicuity in contextual modulation by visual search. Journal of Vision, 11(1):6, p1-11.

Rüter J, Francis G, Frehe P, Herzog MH (2011) Testing dynamical models of vision. Vision Research, 51(3), p343-351.

Chkonia E., Roinishvili M., Makhatadze N., Tsverava L., Stroux A., Neumann K., Herzog M.H., Brand A. (2010). The shine-through masking paradigm is a potential endophenotype of schizophrenia. PLoS ONE, 5(12), e14268.

Team Members Postdoctoral Fellows Céline Cappe Aaron Clarke Karin Pilz Marcus Vergeer

PhD Students Marco Boi Vitaly Chicherov Lukasz Grzeczkowski Mauro Manassi Johannes Rueter Izabela Szumska Evelina Thunell Master Students Julianne Grainger Michel Akselrod Aurelie Papilloud Engineer Marc Repnow Administrative Assistant Laure Dayer

Aydin M, Herzog MH, Ögmen H (2011a) Barrier effects in non-retinotopic feature attribution. Vision Research, 51(16), p1861-1871.

BMI - Brain Mind Institute

Aydin M, Herzog MH, Ögmen H (2011b) Attention modulates spatio-temporal grouping. Vision Research, 51(4), p435-446.

Neural responses for elderly (ELD) and controls (CON) are highly different.

From: Plomp G, Kunchulia M, Herzog MH (2011) Age-related changes in visually evoked electrical brain activity. Hum Brain Mapp. doi: 10.1002-hbm.21273.

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EPFL School of Life Sciences - 2011 Annual Report

Lashuel Lab

http://lashuel-lab.epfl.ch

BMI

Hilal A. Lashuel received his B.Sc. degree in chemistry from the City University of New York in 1994 and his PhD in bio-organic chemistry from Texas A&M University in 2000. In 2001, he moved to Harvard Medical School and the Brigham and Women’s Hospital as a research fellow in the Center for Neurologic Diseases where he was later promoted to an instructor in neurology. In 2005 Dr. Lashuel joined the Brain Mind Institute as a tenure track assistant professor and was promoted in 2011 to an associate professor.

Hilal Lashuel

Associate Professor

Introduction

Current research efforts in our laboratory cover the following topics: (1) Elucidating the molecular and cellular determinants underlying amyloid-β and α-synuclein (α-syn) aggregation and toxicity in Alzheimer’s diseases and Parkinson’s disease (PD) and related disorders. (2) Elucidating the structural basis of amyloid-associated toxicity by correlating the structural properties of defined aggregates in the amyloid pathway to their toxicity in primary neuronal cultures; (3) Developing innovative chemical approaches and novel tools to monitor and control protein folding/ misfolding and self-assembly in vitro and in vivo with spatial and temporal resolution; (4) Understanding the role of post-translational modifications in the pathogenesis of neurodegenerative diseases; (5) Identifying and validating new therapeutic targets for treating PD.

Keywords

Neurodegeneration, Parkinson’s disease, Alzheimer’s disease, chemical biology, amyloid, aggregation, toxicity, fibrils, phosphorylation, kinases, post-translational modifications, semisynthesis.

Results Obtained in 2011

The role of post-translational modifications (PTMs) in the pathogenesis of Parkinson’s disease and related disorders: Detailed understanding of the role of each PTM in α-syn aggregation and toxicity remains elusive, because the natural enzymes involved in regulating these modifications remain unknown. Towards addressing this knowledge gap, our laboratory has developed and optimized for the first time multiple efficient synthetic and semisynthetic approaches that enable site-specific introduction of single or multiple PTMs into α-syn and used these homogeneously modified forms of α-syn to elucidate the effect of all disease-associated modification on the structure, aggregation, membrane binding and subcellular localization of α-syn.

Our studies have provided novel insight into the role of diseases-associated phosphorylation, ubiquitination of α-syn in regulating the structure, aggregation, and membrane binding of α-syn in vitro.

Ubiquitination: The directed site-specific ubiquitination of α-syn at a single or multiple lysine residues has not been possible. To address this problem, we developed, in collaboration with the Brik laboratory a semisynthetic strategy by combining cysteine- and d-mercaptolysine-based methods for native chemical ligation (NCL) for the site-specific incorporation of ubiquitin and the preparation and characterization of highly homogenous monoubiquitinated forms of α-syn. Our results provide strong evidence in support of the hypothesis that the N-terminal ubiquitination of α-syn stabilizes the monomeric form of the protein and thus prevents its oligomerization and fibrillogenesis.

Phosphorylation: Whether phosphorylation enhances or protects against α-syn toxicity in vivo remains unknown. To assess the effect of phosphorylation at S87, we investigated the cellular and behavioral effect of overexpression of wild-type (WT), S87A, and S87E α-syn to block or to mimic S87 phosphorylation, respectively, in the substantia nigra of rats using recombinant adeno-associated vectors. Our results revealed that WT and S87A overexpression induced α-syn aggregation, loss of dopaminergic neurons, and fiber pathology. These neuropathological effects correlated well with the induction of hemi-parkinsonian motor symptoms.

Strikingly, overexpression of the phosphomimic mutant S87E did not show any toxic effect on dopaminergic neurons and resulted in significantly less α-syn aggregates, dystrophic fibers, and motor impairment. Together, our data demonstrate that mimicking phosphorylation at S87 inhibits α-syn aggregation and protects against α-syn-induced toxicity in vivo, suggesting that phosphorylation at this residue could play an important role in controlling α-syn neuropathology. In addition, our results provide strong evidence for a direct correlation between α-syn-induced neurotoxicity, fiber pathology, and motor impairment and the extent of α-syn aggregation in vivo, suggesting that lowering α-syn levels and/or blocking its aggregation are viable therapeutic strategies for the treatment of PD and related synucleinopathies.

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Yu L, Prudent M, Fauvet B, Lashuel HA* and Girault H* “Phosphorylation of α-syn at Y125 and S129 alters its metal binding properties: Implications for understanding the role of a-synuclein in the pathogenesis of Parkinson’s disease and related disorders”. ACS Chem. Neurosci. 2011 2, 667–675.

Jan A, Adolfsson O, Allaman I, Buccarello AL, Magistretti PJ, Pfeifer A, Muhs A, Lashuel HA*, “Aβ42 neurotoxicity is mediated by ongoing nucleated polymerization process rather than by discrete Aβ42 species”. J. Biol. Chem. 2011, 286(10):8585-96.

Hejjaoui H, Haj-Yahya M, Kumar KS, Brik A* and Lashuel HA* “Towards elucidating the role of ubiquitination in the pathogenesis of Parkinson’s disease using semisynthetic ubquitinated α-syn”. Angew Chem Int Ed. 2011, 10;50(2):405-9.

Paleologou KE., Oueslati Abid, Kim H-Y, Lamberto GR., Rospigliosi CC., Schmid A., Chiappe D., Moniatte M., Eliezer D., Zweckstetter M., Masliah E. Lashuel HA*.” Phosphorylation at S87 is enhanced in synucleinopathies, inhibits alphasynuclein oligomerization, and influences synuclein-membrane interactions” J. Neuroscience, 2010, 3;30(9):3184-98.

Siman P, Blatt O, Moyal T, Danieli T, Lebendiker M, Lashuel HA, Friedler A, Brik A. “Chemical synthesis and expression of the HIV-1 Rev Protein” ChemBiochem. 2011, 2;12(7):1097-104.

Team Members Postdoctoral Fellows Baillie Mark Burai Ritwik Mahul Mellier Anne-Laure Oueslati Abid Wang Zheming PhD Students Ansaloni Annalisa Desobry Carole Fares Bilal Fauvet Bruno Hejjaoui Mirva Mbefo Kamdem Martial Vercruysse Filip Master’s Student Ashrafi Amer Research Associates Jordan Nathalie Perrin John Administrative Assistants Favre Sandrine Bouchet Stéphanie

Elturk, Fauvet B, Ouertatani-Sakouhi, Lugari A, Betzi S, Roche P, Morelli X and Lashuel HA*. “ An integrative in silico methodologies for the identification of small molecule inhibitors of Macrophage Migration Inhibitory factor”. J. Bioorg. Chem. 2010, 18(14):5425-40.

Butterfied SM and Lashuel HA*. “Amyloidogenic protein-membrane interactions: mechanistic insights from model systems”. Angewandte Chemie Int Ed. 2010, 49, 5628-5654.

Oueslati A¥, Fournier M¥, and Lashuel HA*. “Role of post-translational modifications in modulating α-syn structure, aggregation and toxicity: implications for Parkinson’s disease pathogenesis and therapies”. Prog Brain Res. 2010;183C:115-145.

BMI - Brain Mind Institute

Our group works at the interface of chemistry and biology to bring to bear the power of chemistry, biophysics, proteomic engineering, and neurobiology to address many of the key outstanding questions and technical challenges in the field of neurodegenerative research.

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EPFL School of Life Sciences - 2011 Annual Report

Luthi-Carter Lab http://lngf.epfl.ch/

BMI

Ruth Luthi-Carter obtained her PhD from Johns Hopkins University and conducted a postdoctoral fellowship at Harvard University’s MassGeneral Institute for Neurodegenerative Diseases, where she was promoted to the rank of Instructor. She joined the Brain Mind Institute as an Assistant Professor in 2003. Prof. Luthi-Carter is an international leader in the application of transcriptomic profiling approaches to understand neurodegenerative diseases and has led several large international consortium projects on HD. Her innovative, unbiased gene expression analysis strategies have established novel paradigms for the implementation of transcriptomic data, and have been successful in elucidating many important new facets of normal and disease-related neuronal function.

Ruth Luthi-Carter Tenure Track Assistant Professor

Introduction

The Laboratory of Functional Neurogenomics (LNGF) uses high-throughput gene expression profiling and other molecular approaches to elucidate new aspects of brain function and neurodegenerative disease. We use this approach to study the diverse effects of pharmacologic agents and disease-causing proteins on the expression of the entire mammalian genome, allowing us understand which molecules might be responsible for a particular brain-related process. Our research focuses primarily on Huntington’s disease (HD), and the function of the striatum and cerebral cortex, the brain regions involved in HD. Other research interests include brain aging, neural cell type-specific aspects of gene expression, and the development of new tools for gene expression analysis and drug discovery.

Understanding diseases with known causes like HD has been viewed as a unique opportunity to elucidate universal mechanisms of neurodegeneration and explore their possible treatment, and we believe that a neuroprotective treatment for Huntington’s disease might not only benefit patients with this disorder, but also be applicable to other, more prevalent diseases.

Keywords

Neurodegenerative disease, Huntington’s disease, striatum, cerebral cortex, motor cortex, aging.

Results Obtained in 2011

This year we continued to make important progress in our search for new therapeutic targets for Huntington’s disease and in developing novel methodologies for improving analyses of gene expression data.

1) Unveiling of Population-Specific Expression Analysis (PSEA), a method to deconvolute molecular expression data into contributions from individual cell types.

Many human diseases are accompanied by histological changes of affected tissues. When performing molecular profiling of such tissues, sample heterogeneity and chang-

es in the cellular composition can obscure and confound the identification of disease-related effects. In order to address this problem, we developed a computational method to resolve gene expression measured in samples of varying composition into the contributions from individual cell populations. This novel method allows identification of cell population-specific changes. We have recently unveiled the PSEA method and its application to human neurodegenerative disease in a publication in Nature Methods (Kuhn et al., 2011).

2) New insights from HD-regulated genes: RGS2 RNA profiling yields valuable information on how cells respond to toxic stimuli. In some cases, changes in gene expression are part a compensatory program, whereas, in others, they are detrimental to the cell. Molecules showing increased and decreased expression can generally be parsed into pathological versus protective changes through examining their contributions to health or toxicity in model systems. These analyses discriminate HD-regulated genes into etiologic, compensatory, and bystander effects (see Figure). Using this approach, we have recently discovered that expression levels of the G-protein signaling regulator RGS2 are inversely correlated with neuronal survival in HD: reversing HD-induced decreases in RGS2 expression enhanced mutant huntingtin’s neurotoxicity, while further decreasing RGS2 using RNAi was neuroprotective. We also discovered a putative mechanism for the RGS2 inhibition’s effect, comprising the activation of the HD-neuroprotective MAP kinase ERK. Our results support the perspective that some changes, even early changes, in gene expression represent compensatory responses of cells to limit diseaserelated neurotoxicity. These recent data also suggest that inhibition of RGS2 may be a rational strategy to achieve neuroprotection in HD (Seredenina et al., 2011).

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Kuhn, A., Thu, D., Waldvogel, H., Faull, R.L.M. and Luthi-Carter, R. Populationspecific expression analysis (PSEA) detect molecular changes in human diseased brain. Nature Methods 8:945-947.

Jiang, M., Wang, J., Fu, J., Du, L., Jeong, H., West, T., Xiang, L., Peng, Q., Hou, Z., Cai, H., Seredenina, T., Arbez, N., Zhu, S., Sommers, K., Qian, J., Zhang, J., Mori, S., Yang, X.W., Tamashiro, K.L., Aja, S., Moran, T.H., Luthi-Carter, R., Martin, B., Maudsley, S., Mattson, M.P., Cichewicz, R.H., Ross, C.A., Holtzman, D.M., Krainc, D., Duan, W. Neuroprotective role of Sirt1 in mammalian models of Huntington’s disease through activation of multiple Sirt1 targets. Nature Medicine 18:153-158.

Seredenina, T., Gokce, O. and Luthi-Carter, R. Decreased striatal RGS2 expression is neuroprotective in Huntington’s disease (HD) and exemplifies a compensatory aspect of HD-induced gene regulation. PLoS ONE e22231.

Labbadia, J.P. Labbadia, Cunliffe, H., Weiss, A., Katsyuba, E., Sathasivam, K., Seredenina, T., Woodman, B., Moussaoui, S., Frentzel, S., Luthi-Carter, R., Paganetti, P. and Bates, G.P. Altered chromatin architecture underlies progressive impairment of the heat shock response in Huntington’s disease mice. J. Clin.

Invest. 121:3306-3319.

Team Members Postdoctoral Fellows Asad Jan Roger Moser Tamara Seredenina David Taylor Doris Chu Voo Thu Erwann Vieu Phd Students Ana Jovicic Irina Krier Technicians Maria De Fatima Rey Lely Feletti Project Students Elias Gebara Elena Katsyuba Julien Fransisco Zaldivar-Jolissaint Administrative Assistant Laure Dayer

Luthi-Carter, R., Taylor, D., Pallos, J., Lambert, E., Amore, A., Parker, A., Moffitt, H., Smith, D.L., Runne, H., Gokce, O., Kuhn, A., Xiang, Z., Maxwell, M.M., Reeves, S.A., Bates, G.P., Neri, C., Thompson, L.M., Marsh, J.L., Kazantsev, A.G. (2010) SIRT2 inhibition achieves neuroprotection by decreasing sterol biosynthesis. Proc. Natl. Acad. Sci. U.S.A. 107:7927-7932.

Gambazzi, L., Gokce, O., Seredenina, T., Katsyuba, E. Runne, H., Markram, H., Giugliano, M. and Luthi-Carter, R. (2010) Diminished activity-dependent BDNF expression underlies cortical neuron microcircuit hypoconnectivity resulting from exposure to mutant huntingtin fragments. J. Pharmacol. Exp. Ther.

335:13-22.

Seredenina, T. and Luthi-Carter, R. (2012) What have we learned from gene expression profiles in Huntington’s disease? Neurobiol. Dis. 45:83-98. [Review article]

BMI - Brain Mind Institute

Luthi-Carter, R. and Kazantsev, A.G. (2010) SIRT2-mediated neuroprotection and cholesterol dyshomeostasis in Huntington’s disease. Proc. Natl. Acad. Sci. U.S.A. 107:E144. [Letter]

Functional significance of Huntington’s disease-related gene expression changes.

The large number of gene expression changes associated with Huntington’s disease can be divided into three categories based on their effects on the disease process (caused by mutant huntingtin (Htt-QQQ)): some are detrimental and mediate neurodegeneration (red); others arise from compensatory responses that counteract mutant Htt toxicity (green); a third subset may be without a functional effect, as judged from the fact that restoring their levels to normal has no apparent impact on disease phenotype (blue).

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EPFL School of Life Sciences - 2011 Annual Report

Magistretti Lab http://lndc.epfl.ch/

BMI

Director of the Brain Mind Institute at EPFL and of the Center for Psychiatric Neuroscience of the University of Lausanne/CHUV. Internationally recognized leader in the field of brain energy metabolism and glia biology. His group has discovered some of the mechanisms that underlie the coupling between neuronal activity and energy consumption by the brain. Since October 2010, director of NCCR SYNAPSY - “The synaptic bases of mental diseases”. Recipient of the Theodore-Ott Prize (1997). International Chair (2007-2008) at the Collège de France, Paris. Since 2010 IBRO Secretary General.

Pierre Magistretti

Full Professor Joint Chair EPFL/UNIL-CHUV

Introduction

We investigate the cellular and molecular mechanisms of brain energy metabolism, in particular the interactions between neurons and astrocytes and the role of this interaction in normal brain function (e.g. learning and memory), as well as dysfunction.

Keywords

Neuroenergetics, neuro-glia interaction, brain metabolism, neuronal and glial plasticity, high-resolution optical imaging, digital holographic microscopy, cell dynamics, neurodegeneration, sleep.

Results Obtained in 2011

Neuroenergetics (Mireille Bélanger and Igor Allaman) Our group and others have contributed to demonstrate that glucose metabolism in astrocytes is predominantly glycolytic, while oxidative metabolism characterizes neurons.

We hypothesize that this limited capacity of neurons to increase their glycolytic rate could be a lower ability to detoxify methylglyoxal (MeG), a toxic by-product of glycolysis. Indeed, the production of MeG in a cell is proportional to the rate of glycolysis as it is estimated that between 0.1% to 0.4% of the glucose entering the glycolytic pathway is inevitably metabolized in the form of MeG. MeG accumulation induces cellular damage (e.g. formation of “advanced glycation end products”, AGEs) leading to apoptosis in different cell types including neurons . The glyoxalase system is the most important pathway for the detoxification of MeG. We observed that both enzymes composing the glyoxalase system (glyoxalase-1 and glyoxalase-2) were highly expressed in primary mouse astrocytes compared to neurons, which translated into higher enzymatic activity rates in astrocytes (9.9-fold and 2.5-fold respectively).

The presence of a highly efficient glyoxalase system in astrocytes was associated with lower accumulation of AGEs compared to neurons, a greater resistance to methylglyoxal toxicity, and the capacity to protect neurons against methylglyoxal in a co-culture system. In addition, we observed that glyoxalase-1 down-regulation, using RNA interference strategies, resulted in a loss of viability in neurons, but

not in astrocytes. Interestingly, we were able to demonstrate that stimulation of neuronal glycolysis via lentiviralmediated over-expression of 6-phosphofructose-2-kinase/ fructose-2,6-bisphosphatase-3 to result in increased methylglyoxal levels and AGEs formation. As a whole our observations suggest that the poor glycolytic capacity of neurons as compared to astrocytes may be related to weaker defense mechanisms against MeG toxicity. Accordingly, the neuroenergetic specialization taking place between these two cell types may serve as a protective mechanism against methylglyoxal-induced neurotoxicity.

Neurophotonic project Neurons are known to be excitable cells, essentially through variations of their membrane potential, which occur through ionic influx and outflux between the cytosol and the extracellular medium. To do that, these cells possess several transmembrane proteins involved in ionic fluxes, such as voltage-gated ion channels or ligand-gated ion channel, in particular glutamatergic receptors (NMDA and AMPA receptors) whose activation is known to be linked with water diffusion and consequent volume changes. Digital Holographic Microscopy (DHM) is not only a non-invasive optical imaging technique that provides quantitative phase images of living cells but also quantitative monitoring of the phase signal by DHM was a simple label-free method to study the effects of glutamate on neuronal optical responses. We have shown that a short application of glutamate (30mM; 30s) produced the following three distinct optical responses in mouse primary cortical neurons in culture, predominantly mediated by NMDA receptors: biphasic, reversible decrease (RD) and irreversible decrease (ID) responses.

Furthermore, we are interested in studying cell volume regulation mechanisms in astrocytes that are closely related to neuronal activity. With a combined DHM/Epifluorescence setup, we are investigating astrocyte cell swelling and ion dynamics in vitro in response to glutamate application and exposure to elevated potassium levels.

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Allaman I, Gavillet M, Bélanger M, Laroche T, Viertl D, Lashuel HA, Magistretti PJ. Amyloid-beta aggregates cause alterations of astrocytic metabolic phenotype: impact on neuronal viability. J Neurosci. 30(9):3326-38 (2010).

Scientists Igor Allaman Nicolas Aznavour Stéphane Chamot Zhizhong Dong Hubert Fiumelli Pascal Jourdain Sylvain Lengacher Pierre Marquet Jean-Marie Petit Jiangyan Yang

Brunet JF, Allaman I, Magistretti PJ, Pellerin L. Glycogen metabolism as a marker of astrocyte differentiation. J Cereb Blood Flow Metab. 30(1):51-5 (2010).

Jolivet R, Allaman I, Pellerin L, Magistretti PJ, Weber B. Comment on recent modeling studies of astrocyte-neuron metabolic interactions. J Cereb Blood Flow Metab. 30(12):1982-6 (2010).

N. Pavillon, A. Benke, D. Boss, C. Moratal, J. Kühn, P. Jourdain, C. Depeursinge, P. J. Magistretti, and P. Marquet, “Cell Morphology and Intracellular Ionic Homeostasis explored with a Multimodal Approach combining Epifluorescence and Digital Holographic Microscopy,” J. Biophotonics 3, 432–436 (2010).

Bélanger M, Allaman I, Magistretti PJ. Differential effects of pro- and antiinflammatory cytokines alone or in combinations on the metabolic profile of astrocytes. J Neurochem. 116(4):564-76 (2011).

Allaman I, Bélanger M, Magistretti PJ. Astrocyte-neuron metabolic relationships: for better and for worse. Trends Neurosci. 34(2):76-87 (2011).

Allaman I, Fiumelli H, Magistretti PJ, Martin JL. Fluoxetine regulates the expression of neurotrophic/growth factors and glucose metabolism in astrocytes.

Psychopharmacology (Berl). 216(1):75-84 (2011).

Lavoie S, Allaman I, Petit JM, Do KQ, Magistretti PJ. Altered glycogen metabolism in cultured astrocytes from mice with chronic glutathione deficit; relevance forneuroenergetics in schizophrenia. PLoS One. 6(7):e22875 (2011).

Bélanger M, Allaman I, Magistretti PJ. Brain energy metabolism: focus on astrocyte- neuron metabolic cooperation. Cell Metab. 14(6):724-38 (2011).

Bélanger M, Yang J, Petit JM, Laroche T, Magistretti PJ, Allaman I. Role of the glyoxalase system in astrocyte-mediated neuroprotection. J Neurosci.

31(50):18338-52 (2011).

Senior Scientist Gabriele Grenningloh

Postdoctoral Fellows Jonas Kühn Mireille Bélanger PhD Students Maxime Baud Daniel Boss Elena Migacheva Julia Parafita Monika Saxena Manuel Zenger Master’s Student Anna Mikhaleva Technicians Cendrine Barrière Aurélie Calame Joel Gyger Evelyne Ruchti Administrative Assistant Egizia Carbone

BMI - Brain Mind Institute

P. Jourdain, N. Pavillon, C. Moratal, D. Boss, B. Rappaz, C. Depeursinge, P. Marquet, and P. J. Magistretti, “Transmembrane water fluxes in neurons revealed by Digital Holographic Microscopy: application to the study of glutamate ionotropic receptors and of the co-transporters KCC2 and NKCC1,” J. Neurosci. 31, 11,846–11,854 (2011).

High expression of Glo-1 in astrocytes of the mouse cerebral cortex. Coronal sections of mouse brain were immunostained with Glo-1 and with the astrocytic marker GFAP. Glo-1 immunoreactivity is located in the cell body and processes along the GFAP+ filaments.

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EPFL School of Life Sciences - 2011 Annual Report

Markram Lab http://bmi.epfl.ch

Henry Markram

BMI

Henry Markram is a professor of the Laboratory for Neural Microcircuitry and director of the Blue Brain Project, which he founded in 2005. He studied medicine and neuroscience at the University of Cape Town and obtained his Ph.D. in Neuroscience at the Weizmann Institute of Science. He worked at the Max Planck Institute, NIH, and WIS. In 2002 he moved to the EPFL to form and direct the Brain Mind Institute. He received numerous awards and published over a 100 papers. He discovered numerous principles governing the architecture of the neocortex (e.g. innate assemblies) and brain plasticity (e.g. Spike Timing Dependent Plasticity, STDP) and proposed the Lego Theory of Memory. He co-developed models of synapses and plasticity, the theory of Liquid Computing, and Intense World Theory of Autism. His is currently mobilizing an international effort to launch the Human Brain Project.

Full Professor

Introduction

The Laboratory of Neural Microcircuitry (LNMC) is dedicated to understanding the structure, function and plasticity of the microcircuitry of the neocortex, the outer, most evolved layer of the mammalian brain. In humans the neocortex constitutes more than 80% of the brain. A detailed description of cortical circuits, their neural constituents at the cellular and synaptic level is a fundamental requirement for understanding the mechanism involved in perception, attention, decision-making, memory formation, higher cognition and complex behaviors. We focus on the rodent (mice and rats) brain.

Keywords

Neurons, synaptic plasticity, neural microcircuits, neuronal coding, patch clamp, signal integration, electrophysiology, single cell gene expression, ion channels, neuron morphology, modeling, autism.

Results Obtained in 2011

To investigate these neocortical microcircuits, we developed state of art technologies including 12 patch-clamp recordings to dissect circuits, single cell RT-PCR to identify genes expressed in specific cells, dynamic patch-clamp to electrically lesion ion channels, multi-electrode recording and stimulation to study the evoked responses of microcircuits in brain slices, automated patch-clamp to study ion channel kinetics. Using these techniques, we tracked the development of the layer 5 pyramidal neuron [1], discovered effective electrical stimuli that are most useful for modeling neurons [2], discovered that neurons are sensitive to the electrical fields generated by other neurons [3], characterized and databased the biophysics of ion channels expressed in cell lines [4], showed that a brief burst in one neuron causes self-inhibition and correlates the surrounding neurons [5], and discovered that the synaptic connectivity between neurons is largely innately determined causing neurons to be clustered in an experience independent manner [6]. In our work on autism, we achieved an even greater level of unification of all findings on autism and described this in The Intense World Theory of Autism [7].

The discovery of innate neural assemblies was a significant recent finding [6]. This study involved the first ever 12 patch-clamp recordings of layer 5 pyramidal neurons. We found that the con-

nectivity between neurons followed a clustering rule where the connection probability and strength of connectivity between any two neurons is positively correlated to the number of their common neighbors. These innate assemblies are independent of experience and hence we proposed that they arise innately during development. The states of the synapses within innate assemblies were not suitable for acquiring new memories, and we therefore proposed that they are elementary building blocks of the neocortex that represent genetically programmed knowledge. We therefore proposed the Lego Theory of Memory [8] where we all have the same types of lego blocks (which would explain why we all perceive the world in the same way), but we can combine them differently during life (which would explain our unique history of memories).

The second important discovery related to ephaptic coupling of neurons [2]. Apart form direct synaptic transmission, it has been speculated that neurons may be influenced by external electrical fields (so-called, LFPs). We used the 12 patch system to record from one neuron and generated electrical fields around the recorded neuron. We found that cortical pyramidal cells are indeed sensitive to the electrical fields generated by other neurons. This finding has enormous potential significance because it means that neurons can become synchronized by waves of these fields throughout the brain without any direct synaptic communication.

The third important discovery related to how a neuron should be probed to extract the mechanisms governing its behavior [3].

We have devised a novel theoretical framework validated experimentally for objectively selecting the stimuli that best unravel the neuron’s dynamics. The general framework that we propose paves the way for defining, evaluating and standardizing effective electrical probing of neurons and thus lays the foundation for a much deeper understanding of neuronal behavior.

We also presently invest considerable effort into developing a new method to obtain the single cell transcriptome (all genes expressed in a single cell), which we believe will allow us to map the neuronal diversity of the brain and predict structural and functional properties of the brain. We are also completing a series of experiments on the animal model of autism exploring how the environment influences the progression of autism.

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Selected Publications

Romand S, Wang Y, Toledo-Rodriguez M, Markram H. Morphological development of thick-tufted layer V pyramidal cells in the rat somatosensory cortex.

Front Neuroanat. 2011, 17;5:5. (1) Anastassiou CA, Perin R, Markram H, Koch C. Ephaptic coupling of cortical neurons. Nature Neurosci. 2011;14(2):217-23. (2) Druckmann S, Berger TK, Schürmann F, Hill S, Markram H, Segev I. Effective stimuli for constructing reliable neuron models. PLoS Comput Biol.

2011;7(8):e1002133. (3) Ranjan R, Khazen G, Gambazzi L, Ramaswamy S, Hill SL, Schürmann F, Markram H. Channelpedia: an integrative and interactive database for ion channels. Front Neuroinform. 2011;5:36. (4) Berger TK, Silberberg G, Perin R, Markram H. Brief bursts self-inhibit and correlate the pyramidal network. PLoS Biol. 2010;8(9). (5) Perin R, Berger TK, Markram H. A synaptic organizing principle for cortical neuronal groups. PNAS, 2011;108(13):5419-24. (6) Markram K, Markram H. The intense world theory - a unifying theory of the neurobiology of autism. Front Hum Neurosci. 2010;4:224. (7) Markram H, Perin R. Innate neural assemblies for lego memory. Front Neural Circuits. 2011;5:6. 2011. (8)

Team Members Group leaders Abdeladim Elhamdani Kamila Markram Jesper Ryge Postdoctoral Fellows Emmanuelle Logette Rodrigo Perin Séverine Petitprez Maurizio Pezzoli Susana Camacho PhD Students Vincent Delattre Monica Favre Jean-Pierre Ghobril Shruti Muralidhar Rajnish Ranjan Master’s Students Michela Abele Micheal Schartner Technicians Deborah La Mendola Julie Meystre Chantal Moratal Clément Murgues Coraly Pernet Apprentice Eliott Mutrux Researchers Harald Holze Ying Shi Visiting researcher Costas Anastassiou Internships Dimitri Christodoulou Stéphanie Davis Olivier Hagens Mirija Herzog Cécile Prébandier Louis Wessels

BMI - Brain Mind Institute

Administrative Assistant Christiane Debono

Multi-neuron patch-clamp: A, biocytin labeling of 12 neurons recorded simultaneously; B, Region of the brain from which brain slices where obtained and neurons recorded; C, 3D anatomical reconstruction of 12 recorded pyramidal neurons.

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EPFL School of Life Sciences - 2011 Annual Report

Moore Lab

http://moorelab.epfl.ch

BMI

Darren Moore conducted his PhD in molecular neuroscience at the University of Cambridge (1998-2002) and post-doctoral research on familial Parkinson’s disease (2002-05) in the Department of Neurology at the Johns Hopkins University School of Medicine. He spent 3 years on the Neurology faculty at Johns Hopkins as an Instructor (2005-06) and later as Assistant Professor (2006-08). Prof. Moore established the Laboratory of Molecular Neurodegenerative Research at EPFL in 2008 to focus on understanding the molecular basis of Parkinson’s disease and related neurodegenerative disorders.

Darren Moore Tenure Track Assistant Professor

Introduction

a simple model in the baker’s yeast, Saccharomyces cerevisiae, to further understand the molecular pathobiology of LRRK2 and we have used this model to identify genes that can modify LRRK2-dependent phenotypes. One of these gene products, the GTPase-activating protein ArfGAP1, interacts with LRRK2 and regulates its enzymatic activity and neuronal toxicity whereas ArfGAP1 also serves as a novel substrate of phosphorylation by LRRK2. Finally, our research is attempting to clarify the mechanisms underlying neuronal cell death induced by mutated LRRK2 and here we continue to focus on the role of mitochondrial dysfunction, autophagy, neuronal morphology and proteins or protein complexes that interact with, or are phosphorylated by, LRRK2.

Keywords

In 2011 we continued to focus on the ATP13A2 protein.

Genetic mutations in ATP13A2 cause familial PD and Kufor-Rakeb syndrome, a juvenile-onset, autosomal recessive disorder characterized by pallido-pyramidal neurodegeneration with severe parkinsonism and dementia. ATP13A2 is a novel P 5 -type ATPase protein which is thought to transport cations across intracellular vesicular membranes in an ATP-dependent manner. We are attempting to understand the normal function of ATP13A2 in neurons, and we are also creating disease models based upon gene disruption or silencing to replicate the effects of recessive “lossof-function” mutations.

The Laboratory of Molecular Neurodegenerative Research investigates the pathophysiology of Parkinson’s disease, a chronic neurodegenerative movement disorder. Our laboratory investigates the normal biological function and pathological dysfunction of various proteins, that when genetically mutated, cause an inherited (familial) form of Parkinson’s disease. Our mission is to understand the molecular mechanisms and pathways through which disease-associated mutations in these proteins cause neuronal damage and neurodegeneration. We aim to use this information in the long term to develop novel therapies and neuroprotective strategies to delay or prevent this devastating disease.

Parkinson’s disease, parkinsonism, neurodegeneration, genetic mutations, disease models, neuronal cell death, LRRK2, alpha-synuclein, ATP13A2, parkin, VPS35, therapeutic targets, mouse models.

Results Obtained in 2011

The Moore laboratory focuses its investigations on a number of gene products that when mutated cause familial Parkinson’s disease (PD), including leucine-rich repeat kinase 2 (LRRK2), alpha-synuclein, parkin, ATP13A2 and VPS35.

Mutations in the LRRK2, alpha-synuclein and VPS35 genes cause autosomal dominant forms of PD, whereas parkin and ATP13A2 mutations cause autosomal recessive PD. Mutations in the LRRK2 gene were discovered in 2004 and we have been working over the years to model the pathogenic effects of these dominant mutations. In 2011, we continued to develop and phenotype a collection of novel transgenic mice that we created to over express diseaseassociated mutated forms of human LRRK2 protein in the brain. These transgenic models develop some key features of PD with advanced age and will prove extremely useful for understanding how LRRK2 mutations cause neurodegenerative disease. We also conducted genetic interaction studies in mice to reveal that alpha-synuclein-related neuropathology that develops in transgenic mice occurs independent of LRRK2 expression. We recently developed

We are also interested in the role of the E3 ubiquitin ligase, parkin, in mitochondrial function. Genetic mutations in parkin cause early-onset, autosomal recessive PD. Recent studies have shown that parkin translocates to damaged mitochondria to mediate their removal by autophagy (termed mitophagy). We have recently established that parkin can mediate the ubiquitination and proteasomal degradation of mitofusin 1, a protein that normally promotes mitochondrial fusion. Our studies reveal some of the molecular details underlying parkin-dependent mitophagy and support a model whereby, during mitochondrial damage, parkin inhibits mitochondrial fusion through degradation of mitofusin 1 to limit mitochondrial refusion and thereby isolate damaged mitochondria for removal by mitophagy.

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Tsika E, Moore DJ. Mechanisms of LRRK2-mediated neurodegeneration. Curr.

Neurol. Neurosci. Rep. 2012, Epub Mar 24.

Daher JPL, Pletnikova O, Biskup S, Musso A, Gellhaar S, Galter D, Troncoso JC, Lee MK, Dawson TM, Dawson VL, Moore DJ. Neurodegenerative phenotypes in an A53T ?-synuclein transgenic mouse model are independent of LRRK2. Hum. Mol. Genet. 2012,Epub Mar 7.

Stafa K, Trancikova A, Webber PJ, Glauser L, West AB, Moore DJ. GTPase activity and neuronal toxicity of Parkinson’s disease-associated LRRK2 is regulated

by ArfGAP1. PLoS Genet. 2012, 8: e1002527.

Ramonet D, Podhajska A, Stafa K, Sonnay S, Trancikova A, Tsika E, Pletnikova O, Troncoso JC, Glauser L, Moore DJ. PARK9-associated ATP13A2 localizes to intracellular acidic vesicles and regulates cation homeostasis and neuronal integrity. Hum. Mol.Genet. 2012, 21: 1725-43.

Trancikova A, Tsika E, Moore DJ. Mitochondrial dysfunction in genetic animal models of Parkinson’s disease. Antioxid. Redox Signal. 2012, 16: 896-919.

Team Members Post doctoral Fellows Roger Moser Alzbeta Trancikova Elpida Tsika PhD Students Alice Biosa Alessandra Musso Agata Podhajska Klodjan Stafa Master’s Students Duygu Deniz Bas Caroline Shi-Yan Foo Meghna Kannan Sarah Sonnay Anastasia Vishnevetsky Laboratory technician Liliane Glauser Administrative assistant Caroline Rheiner

Glauser L, Sonnay S, Stafa K, Moore DJ. Parkin promotes the ubiquitination & degradation of the mitochondrial fusion factor mitofusin 1. J. Neurochem.

2011, 118: 636-45.

Ramonet D, Daher JPL, Lin BM, Stafa K, Kim J, Banerjee R, Westerlund M, Pletnikova O, Glauser L, Yang L, Liu Y, Swing DA, Beal MF, Troncoso JC, McCaffery JM, Jenkins NA, Copeland NG, Galter D, Thomas B, Lee MK, Dawson TM, Dawson VL, Moore DJ. Dopaminergic neuronal loss, reduced neurite complexity and autophagic abnormalities in transgenic mice expressing G2019S mutant LRRK2. PLoS One 2011, 6: e18568.

Dusonchet J, Kochubey O, Stafa K, Young SM, Zufferey R, Moore, DJ, Schneider BL, Aebischer, P. A rat model of progressive nigral neurodegeneration induced by the Parkinson’s disease-associated G2019S mutation in LRRK2. J. Neurosci.

2011, 31(3): 907-12.

BMI - Brain Mind Institute

Xiong Y, Coombes CE, Kilaru A, Li X, Gitler AD, Bowers WJ, Dawson VL, Dawson TM, Moore DJ. GTPase activity plays a key role in the pathobiology of LRRK2. PLoS Genetics 2010, 6(4):e1000902.

Models of familial Parkinson’s disease: (A) phospho-proteome profiling, (B) dopaminergic neuronal loss, (C) accumulation of autophagosomes, in LRRK2 transgenic mice. (D) Adenoviral-mediated LRRK2 expression in cultured dopaminergic neurons (TH). Lower panel: protein architecture of LRRK2.

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EPFL School of Life Sciences - 2011 Annual Report

Petersen Lab http://lsens.epfl.ch/

BMI

Carl Petersen obtained a BA in Physics from Oxford University in 1992 and his PhD from Cambridge University in 1996 studying calcium signalling under the supervision of Prof. Michael Berridge. As a postdoctoral fellow he worked with Prof. Roger Nicoll investigating synaptic transmission and plasticity at the University of California San Francisco (1996-1998) and with Prof. Bert Sakmann studying neocortical circuits underlying sensory processing at the Max Planck Institute for Medical Research in Heidelberg (1999-2003).

Carl Petersen currently investigates the synaptic mechanisms of sensory perception at the Brain Mind Institute of the EPFL, which he joined in 2003 as an Assistant Professor and in 2010 was promoted to Associate Professor.

Carl Petersen

Associate Professor

Introduction

The Laboratory of Sensory Processing aims to obtain a causal and mechanistic understanding of sensory perception and associative learning at the level of individual neurons and their synaptic interactions within complex neural circuits of the mammalian brain. Our experiments investigate tactile sensory perception in the mouse whisker sensorimotor system.

Keywords

Sensory perception, active sensing, motor control, rewardbased learning, whole-cell recordings, optogenetics, voltage-sensitive dye imaging, two-photon microscopy.

Results Obtained in 2011

Active Touch (Crochet et al., 2011): Sensory information is actively gathered by animals, but the synaptic mechanisms driving neuronal circuit function during active sensory processing are poorly understood. In this study, we investigated the synaptically driven membrane potential dynamics during active whisker sensation using whole-cell recordings from layer 2/3 pyramidal neurons in the primary somatosensory barrel cortex of behaving mice. Although whisker contact with an object evoked rapid depolarization in all neurons, these touch responses only drove action potentials in 10% of the cells. Such sparse coding was ensured by cell-specific reversal potentials of the touch-evoked response that were hyperpolarized relative to action potential threshold for most neurons.

Intercontact interval profoundly influenced touch-evoked postsynaptic potentials, interestingly without affecting the peak membrane potential of the touch response. Dual whole-cell recordings indicated highly correlated membrane potential dynamics during active touch. Sparse action potential firing within synchronized cortical layer 2/3 microcircuits therefore appears to robustly signal each active touch response.

sory perception. Synaptic transmission between identified neurons within neocortical microcircuits has mainly been studied in brain slice preparations in vitro. In this study, we investigated brain-state-dependent neocortical synaptic interactions in vivo by combining the specificity of optogenetic stimulation with the precision of whole-cell recordings from postsynaptic excitatory glutamatergic neurons and GFP-labeled inhibitory GABAergic neurons targeted through two-photon microscopy. Channelrhodopsin-2 (ChR2) stimulation of excitatory layer 2/3 barrel cortex neurons evoked larger and faster depolarizing postsynaptic potentials and more synaptically driven action potentials in fast-spiking (FS) GABAergic neurons compared to both non-fast-spiking (NFS) GABAergic neurons and postsynaptic excitatory pyramidal neurons located within the same neocortical microcircuit. The number of action potentials evoked in ChR2-expressing neurons showed low trial-totrial variability, but postsynaptic responses varied strongly with near-linear dependence upon spontaneously driven changes in pre-stimulus membrane potential. Postsynaptic responses in excitatory neurons had reversal potentials, which were hyperpolarized relative to action potential threshold and were therefore inhibitory. Reversal potentials measured in postsynaptic GABAergic neurons were close to action potential threshold. Postsynaptic inhibitory neurons preferentially fired synaptically driven action potentials from spontaneously depolarized network states, with stronger state-dependent modulation in NFS GABAergic neurons compared to FS GABAergic neurons. Inhibitory neurons appear to dominate neocortical microcircuit function, receiving stronger local excitatory synaptic input and firing more action potentials compared to excitatory neurons. In mouse layer 2/3 barrel cortex, we propose that strong state-dependent recruitment of inhibitory neurons drives competition among excitatory neurons enforcing sparse coding.

In vivo optogenetic probing of cortical synaptic microcircuits (Mateo et al., 2011): Synaptic interactions between excitatory and inhibitory neocortical neurons are important for mammalian sen-

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Selected Publications

Mateo C, Avermann M, Gentet LJ, Zhang F, Deisseroth K, Petersen CCH (2011) In vivo optogenetic stimulation of neocortical excitatory neurons drives brainstate-dependent inhibition. Curr Biol 21: 1593-1602.

Crochet S, Poulet JFA, Kremer Y, Petersen CCH (2011) Synaptic mechanisms underlying sparse coding of active touch. Neuron 69: 1160-1175.

Petersen CCH (2011) Voltage-sensitive dye imaging of cortical spatiotemporal dynamics in awake behaving mice. Chapter in ‘Imaging in neuroscience’. Edited by Fritjof Helmchen and Arthur Konnerth. Published by Cold Spring Harbor Laboratory Press.

Matyas F, Sreenivasan V, Marbach F, Wacongne C, Barsy B, Mateo C, Aronoff R, Petersen CCH (2010) Motor control by sensory cortex. Science 330: 12401243.

Gentet LJ, Avermann M, Matyas F, Staiger JF, Petersen CCH (2010) Membrane potential dynamics of GABAergic neurons in the barrel cortex of behaving mice. Neuron 65: 422-435.

Team Members Postdoctoral Fellows Sylvain Crochet Emmanuel Eggermann Luc Gentet Natalya Korogod Yves Kremer Alexandros Kyriakatos Szabolcs Olah Shankar Sachidhanandam Nadia Urbain Takayuki Yamashita PhD Students Aurelie Pala Varun Sreenivasan Administrative Assistants Séverine Janot Monica Navarro

Aronoff R, Matyas F, Mateo C, Ciron C, Schneider B, Petersen CCH (2010) Longrange connectivity of mouse primary somatosensory barrel cortex. Eur J Neurosci 31: 2221-2233.

BMI - Brain Mind Institute

Grinvald A, Petersen CCH (2010) Imaging the dynamics of neocortical population activity in behaving and freely moving mammals. Chapter in ‘Membrane potential imaging in the nervous system’. Edited by Marco Canepari and Dejan Zecevic. Published by Springer.

The light-gated ion channel, Channelrhodopsin-2(ChR2-YFP), was expressed in excitatory layer 2/3 (L2/3) neurons of mouse barrel cortex using a lentivirus. Blue light evoked depolarisation and action potential firing in ChR2-expressing neurons recorded in vivo. Adapted from Mateo et al., 2011.

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EPFL School of Life Sciences - 2011 Annual Report

Sandi Lab

http://lgc.epfl.ch/

BMI

Carmen Sandi investigates how stress affects brain function, behavior and cognition, with a recent strong interest in understanding stress effects in social behaviors and aggression. Her work has been pioneering in implicating stress hormones and cell adhesion molecules in memory formation and psychopathology. Currently, she is the Chief Editor of the journal Frontiers in Behavioral Neuroscience, Scientific Advisor at the European College of Neuropsychopharmacology, the President of the European Brain and Behavior Society (EBBS) and the Coordinator of the FP7 EU Project MemStick. Prof. Sandi joined the EPFL in 2003 and was promoted to full professor in 2012.

Carmen Sandi Full Professor

Introduction/Results Obtained in 2011

Evidence for biological roots in the transgenerational transmission of intimate partner violence Intimate partner violence is a ubiquitous and devastating phenomenon for which effective interventions and a clear etiological understanding are still lacking. A major risk factor for violence perpetration is childhood exposure to violence, prompting the proposal that social learning is a major contributor to the transgenerational transmission of violence. Using an animal model devoid of human cultural factors, we showed that male rats became highly aggressive against their female partners as adults after exposure to non-social stressful experiences in their youth. Their offspring also showed increased aggression towards females in the absence of postnatal father-offspring interaction or any other exposure to violence. Both the females that cohabited with the stressed males and those that cohabited with their male offspring showed behavioral, physiological and neurobiological symptoms resembling the alterations described in abused and depressed women. With the caution required when translating animal work to humans, our findings extend current psychosocial explanations of the transgenerational transmission of intimate partner violence by strongly suggesting an important role for biological factors.

We are currently investigating the modulatory role of personality traits in the prediction of social hierarchy outcome in rodents and humans. We have identified anxiety trait as a key modulatory factor in the development of either subordinate or dominant status. Our results highlight interactions between the GABAergic and mesolimbic dopaminergic systems as the critical substrates.

The impact of developmental stress on aggression Stress is an important risk factor for a wide variety of psychopathological alterations. In particular, adverse experiences during childhood and adolescence have been associated with the development of psychiatric disorders. We have developed an animal model that recapitulates alterations in orbitofrontal-amygdala interactions observed in humans. We found changes in serotonergic pathways and their epigenetic control in the long-term effects of stress, along with alterations in impulsive behaviors and cognitive bias towards social threats and adversity.

Keywords

Stress, anxiety, aocial hierarchy, aggression, transgenerational mechanisms, epigenetics, early life trauma.

Stress, Personality Traits and Social Hierarchies – Neurobiological Mechanisms Social hierarchies are highly relevant for both individuals’ behavior and physical and mental health, as well as for the well-being of societies. Given that once established, hierarchies tend to be quite stable, the outcome of an initial encounter between two or more individuals can have important consequences for future behavioral interactions and fitness. Our previous work has characterized the effect of stress in the establishment of social hierarchies and identified key neurobiological mechanisms translating stress effects.

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Team Members

Conboy L., Varea E., Castro J.E., Sakouhi-Ouertatani H., Calandra T., Lashuel H. and Sandi C. (2011) Macrophage migration inhibitory factor (MIF) is critically involved in basal and fluoxetine-stimulated adult hippocampal cell proliferation and in anxiety, depression and memory related behaviours. Molecular Psychiatry 16: 533-547.

External Employee Maria Isabel Cordero

Postdoctoral Fellows Martina Fantin Fiona Hollis Guillaume Poirier Ricardo Ramires Yannick Sevelinge Michael van der Kooij

Kraev I., Henneberger C., Rossetti C., Conboy L., Kohler L.B., Fantin M., Jennings A., Venero C., Popov V., Rusakov D., Stewart M.G., Bock E., Berezin V. and Sandi C. (2011) A peptide mimetic targeting of trans-homophilic NCAM binding sites promotes spatial learning and synaptic plasticity in the hippocampus. PloS One, 6(8): e23433. doi:10.1371/journal.pone.0023433.

PhD Students Stamatina Tzanoulinou Vandana Veenit

Bisaz R., Schachner M. and Sandi C. (2011) Causal evidence for the involvement of the neural cell adhesion molecule, NCAM, in chronic stress-induced cognitive impairments. Hippocampus 21: 56-71.

Lab Technicians Christelle Albac CĂŠline Fournier Jocelyn Grosse Coralie Siegmund Olivia Zanolettir

Cuesto G., Enriquez-Barreto L., Carames C., Cantarero M., Gasull X., Sandi C., Ferrus A., Acebes A. and Morales M. (2011) PI3K activation controls synaptogenesis and spinogenesis in hippocampal neurons. Journal of Neuroscience 31: 2721-2733.

Sandi C. (2011) Glucocorticoids act on glutamatergic pathways to affect memory processes. Trends in Neuroscience 34: 165-176.

Luksys G. and Sandi C.* (2011) Neural mechanisms and computations underlying stress effects on learning and memory. Current Opinion in Neurobiology, Epub ahead of print, PMID: 21501959.

Sandi C. (2011) Healing anxiety disorders with glucocorticoids. Proc. Natl.

Acad. Sci. USA 108: 6343-6344. Conboy L. and Sandi C. (2010) Stress at learning facilitates memory formation by regulating AMPA receptor trafficking through a glucocorticoid action. Neuropsychopharmacology 35: 674-685.

Salehi B., Cordero M.I. and Sandi C. (2010) Learning under stress: The invertedU-shape function revisited, Learning & Memory 17:522-530.

Master Student Xavier Fontana

Trainees Eleni Batzianouli Lejla Colic Hussein Khdour Manila Loi Laura Lozano Emil Polny Zhiva Skachokova Students Nicolas Chatel Elise Gehring Damien Huzard Alain Jacot-Guillarmod Chenyu Lin Martin Vogel Administrative Assistant Barbara Goumaz

BMI - Brain Mind Institute

Timmer M., Cordero M.I., Sevelinge Y. and Sandi C. (2011) Evidence for a role of oxytocin receptors in the long-term establishment of dominance hierarchies.

Neuropsychopharmacology, doi:10.1038/ npp.2011.125.

Expression of the immediate early gene c-fos in the rat brain after stress challenge.

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EPFL School of Life Sciences - 2011 Annual Report

Schneggenburger Lab http://www.lsym.epfl.ch

BMI

Ralf Schneggenburger obtained a PhD in Biology at the University of Göttingen in 1993. During post-doctoral stages at the University of Saarland and at the Ecole Normale Supérieure (1994 - 1996), he investigated the role of glutamate receptors in neuronal Ca2+ signaling. As a postdoctoral fellow and as a Research Group Leader at the Max-Planck Institute for biophysical Chemistry (Göttingen, 1996- 2005), he developed a research program in transmitter release mechanisms, and presynaptic plasticity. In 2005, he was appointed as Associate Professor at EPFL and has since then been leading the Laboratory for Synaptic Mechanisms at the Brain Mind Institute. In 2012, he was promoted to Full Professor.

Ralf Schneggenburger Full Professor

Introduction

terminals. Furthermore, re-expressed Syt2 fully rescued a more than 500-fold reduction of Ca2+-evoked transmitter release in Syt2 knock-out mice. This allowed us to begin a structure-function analysis of Syt2 function under direct control of presynaptic Ca2+ concentrations as afforded by the calyx of Held synapse. Our data shows that Syt2, and in analogy Syt1 in forebrain synapses, triggers a fast phase of release which is highly non-linearly dependent on the intracellular Ca2+ concentration, [Ca2+]i (a 4th power relation between [Ca2+]i and release). At the same time, we found that Syt2 suppresses release evoked by low [Ca2+]i elevations, and spontaneous release. This “release clamping” function involves a different part of the Syt2 protein, and probably an interaction with a yet unidentified Ca2+ sensor for slow release. The feasibility of virus-mediated rescue of Synaptotagmin function at the calyx of Held synapse will be the basis for future studies investigating the molecular and biophysical mechanisms of the highly nonlinear Ca2+ dependence of vesicle fusion.

Keywords

In a separate study in 2011, we used Cre-lox mediated conditional removal of floxed genes in mice, to study the role of RIM proteins for presynaptic Ca2+ channels and transmitter release. RIM (for Rab3-interacting molecule) is coded by two major genes (Rim1, 2). In a collaborative research effort, we produced auditory-system specific conditional RIM1/2 knock-out mice, in which mouse survival was not impaired (Han et al., 2011). This allowed us to study the function of RIM proteins in direct presynaptic recordings at the calyx of Held. We found that RIM proteins are necessary to achieve a high density of presynaptic Ca2+ channels, and for vesicle docking at the active zone (Han et al., 2011). The conditional mouse knock-out approach at the calyx of Held synapse will be invaluable for future studies investigating functional parameters of presynaptic proteins.

The main interest of the lab lies in understanding the cellular and molecular mechanisms of neuronal communication at synapses. Nerve cells are arranged in intricate neuronal networks, and communicate with each other at synapses, the contact points between a pre- and postsynaptic neuron pair. Synaptic transmission is mediated by transmitter release in a process of SNARE-protein mediated vesicle fusion, which is controlled by intracellular Ca2+ ions on time scales of a millisecond or less. We also investigate how the functional properties of synapses, including synaptic strength and speed of transmitter release, are specified during the development of neuronal circuits. Understanding the molecular mechanisms of synaptic transmission and synapse development is important to gain insight into neuronal network function, and forms the basis for understanding the pathophysiology of neuropsychiatric and neurodegenerative disorders, many of which represent diseases of the synapse.

Synaptic transmission, nerve terminal, neurotransmitter, exocytosis, short-term plasticity, synapse development.

Results Obtained in 2011

We use an exceptionally large synapse located in the auditory pathway, the calyx of Held, at which we can gain excellent access to the physiology of the presynaptic nerve terminal. In 2011, we could study the function of the Ca2+ sensor protein, Synaptotagmin-2 (Syt2), in triggering a fast phase of vesicle fusion, as well as in suppressing background spontaneous release (Kochubey and Schneggenburger 2011). This study was made possible by adapting methods of virus-mediated protein overexpression in specific mouse brain circuits (see Figure). We found that recombinantly expressed Syt2 is correctly targeted to nerve terminals, including the large calyx of Held

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EPFL School of Life Sciences - 2011 Annual Report

Selected Publications

Kochubey O., Lou X., Schneggenburger R. (2011) Regulation of transmitter release by Ca2+ and synaptotagmin: insights form a large CNS synapse. Trends Neurosci. 34(5), 237-246.

Kochubey O., Schneggenburger R. (2011) Synaptotagmin increases the dynamic range of synapses by driving Ca2+-evoked release and by clamping a nearlinear remaining Ca2+ sensor. Neuron. 2011 Feb 24;69(4):736-48.

Han, Y., Kaeser, P.S., Südhof, T.C., Schneggenburger, R. (2011) RIM Determines Ca2+ Channel Density and Vesicle Docking at the Presynaptic Active Zone.

Neuron 69 : 304-316.

Beurg, M., Michalski, N., Safieddine, S., Bouleau, Y., Schneggenburger, R., Chapman, E. R., Petit, C., and Dulon, D. (2010). Control of exocytosis by synaptotagmins and otoferlin in auditory hair cells. J. Neuroscience 30, 1328113290.

Xiao, L., Han, Y., Runne, H., Murray, H., Kochubey, O., Lüthi-Carter, R. and Schneggenburger, R. (2010) Developmental expression of Synaptotagmin isoforms in single calyx of Held-generating neurons. Mol Cell Neurosci 44: 374-85.

Team Members Postdoctoral Fellows Norbert Babai Naila Ben Fredj Olexiy Kochubey Nicolas Michalski Le Xiao Phd Students Ozgür Genc Enida Gjoni Yunyun Han Elin Kronander Shovan Naskar Technicians Heather Murray Jessica Perritaz Administrative Assistant Laure Dayer

BMI - Brain Mind Institute

Müller, M., Goutman, J. D., Kochubey O., Schneggenburger R. (2010). Interaction between facilitation and depression at a large CNS synapse reveals mechanisms of short-term plasticity. J Neurosci 30(6): 2007-2016.

Virus-mediated protein overexpression in the auditory system. An adenovirus vector drove the expression of GFP (green) and Syt2 (red); note that Syt2 protein was specifically targeted to nerve terminals.

Taken from Kochubey and Schneggenburger 2011, Neuron.

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EPFL School of Life Sciences - 2011 Annual Report

Blue Brain Project http://bluebrain.epfl.ch

Henry Markram

BMI

Henry Markram is a professor of the Laboratory for Neural Microcircuitry and director of the Blue Brain Project, which he founded in 2005. He studied medicine and neuroscience at the University of Cape Town and obtained his Ph.D. in Neuroscience at the Weizmann Institute of Science. He worked at the Max Planck Institute, NIH, and WIS. In 2002 he moved to the EPFL to form and direct the Brain Mind Institute. He received numerous awards and published over a 100 papers. He discovered numerous principles governing the architecture of the neocortex (e.g. innate assemblies) and brain plasticity (e.g. Spike Timing Dependent Plasticity, STDP) and proposed the Lego Theory of Memory. He co-developed models of synapses and plasticity, the theory of Liquid Computing, and Intense World Theory of Autism. His is currently mobilizing an international effort to launch the Human Brain Project.

Full Professor Director BBP

Introduction

The combination of experiment and theory has long formed the basis of the scientific method. As computers become faster, computer simulations – combining experimental measurements and theoretical models – are beginning to capture the biological complexity of the brain. This is the goal of the Blue Brain Project, now in its seventh year. Over this time the project has constructed a prototype brain simulation facility with the software tools, the knowhow and the supercomputing infrastructure to build unifying models of the detailed structure of neuronal circuits and to simulate the way they function.

Keywords

Neocortex, simulation-based research, reverse engineering, high performance computing, unifying models, cortical column, mesocircuits, human brain project

Results Obtained in 2011

2011 was a year of important change for the Blue Brain Project. Due to the mandate of the ETH Board the project prepared itself for future growth and sustainability. In that regard several senior researchers and engineers came on board to bring the project on the road from the proof-ofconcept work of the previous years to a state where the facility can be eventually available for the wider community.

To accommodate this growth, the project moved to its new space in the Quartier Innovation, where all the efforts can be effectively coordinated in a tailored space.

On the scientific side, several important results where published during the year. On the one hand, the previously published series of technical publications on establishing a data-driven, automatic workflow to modeling detailed conductance-based models of individual cells has been complemented with two PLoS Computational Biology studies. In one of them, the method was successfully applied to create and validate the most comprehensive model

of a layer 5 pyramidal cell to date, capable of reproducing multiple somatic and dendritic experimental properties in a unifying model. Secondly, the method was used to explore in silico which experimental stimulation protocol is most effective to constrain detailed models.

Furthermore, in the publication of Khazen et al., we were able to show informatically that a neuron’s features, such as its cortical layer, morphological type and electrical class are informative about the expression of certain gene combinations. Based on the classification data alone, we could predict previously measured ion channel patterns with 78 per cent accuracy. When we added in a subset of data about the ion channels to the classification data, we were able to boost that accuracy to 87 per cent for the more commonly occurring neuronal types. Systematically testing which ion channels were the most informative about others, allowed us to extract logical rules as to which channels co-express or which exclude each other in the different cell types.

Lastly, the year 2011 saw intensive and exciting efforts for the preparation for a 10 year FET Flagship project: in the context of the Human Brain Project – Preparatory Study (HBP-PS) - a one year EU-funded Coordinating Action, nearly three hundred experts in neuroscience, medicine and computing came together to develop a new “ICT-accelerated” vision for brain research and its applications.

The Human Brain Project should lay the technical foundations for a new model of ICT-based brain research, driving integration between data and knowledge from different disciplines, and catalyzing a community effort to achieve a new understanding of the brain, new treatments for brain disease and new brain-like computing technologies. The selection process for the FET Flagship candidates continues in 2012.

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Selected Publications

Team Members

Eilemann S, Bilgili A, Abdellah M, Hernando J, Makhinya M, Pajarola R, and Schürmann F (2012). Parallel Rendering on Hybrid Multi-GPU Clusters, EGPGV 2012.

Project Managers Buncic Nenad Marc-Oliver Gewaltig Sean Hill Eilif Muller Julian Shillcock

Khazen G, Hill S L, Schürmann F, and Markram H (2012). Combinatorial Expression Rules of Ion Channel Genes in Juvenile Rat (Rattus norvegicus) Neocortical Neurons, PLoS One. 2012;7(4):e34786. Epub 2012 Apr 11.

Ramaswamy S, Hill SL, King JG, Schürmann F, Wang Y, Markram H (2012).

Intrinsic Morphological Diversity of Thick-tufted Layer 5 Pyramidal Neurons Ensures Robust and Invariant Properties of in silico Synaptic Connections. J Physiol. 2012 Feb 15;590(Pt 4):737-52. Epub 2011 Nov 14.

Lasserre S, Hernando J, Hill S, Schürmann F, Anasagasti PM, Abou-Jaoudé G and Markram H (2012). A Neuron Membrane Mesh Representation for Visualization of Electrophysiological Simulations, IEEE Transactions on Visualization and Computer Graphics, 18(2):214-217.

Hay E., Hill S., Schürmann F., Markram H, Segev I (2011). Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties. PLoS Computational Biology 7(7): e1002107. doi:10.1371/journal.pcbi.1002107.

Druckmann S, Berger TK, Schürmann F, Hill S, Markram H and Segev I (2011), Effective stimuli for constructing reliable neuron models, Plos Computational Biology, 7(8): e1002133. doi:10.1371/journal.pcbi.1002133.

Hines M, Kumar S and Schürmann F (2011). Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer. Front. Comput. Neurosci.

5:49. doi: 10.3389/fncom.2011.00049.

Ranjan R, Khazen G, Gambazzi L, Ramaswamy S, Hill SL, Schürmann F, and Markram H (2011). Channelpedia: an integrative and interactive database for ion channels, Front. Neuroinform. 5:36. doi: 10.3389/fninf.2011.00036.

General Project Manager Felix Schürmann

Senior Science Writer Richard Walker Operations Alejandro Schiliuk Postdoctoral Fellows Guy Antoine Atenekeng Ahmet Bilgili Joe Graham Daniel Keller Sébastien Lasserre Martin Telefont Werner Van Geit Research Assistants Marija Rakonjac Melissa Cochrane Engineers Marwan Abd Ellah Carlos Aguado Sanchez Athanassia Chalimoudra Jean-Denis Courcol Fabien Delalondre Stefan Eilemann Valentin Haenel John Kenyon (till March) James Gonzalo King Bruno Ricardo Magalhaes Gabriel Mateescu Jeff Muller Keerthan Muthurasa Barthélémy Von Haller PhD Students Georges Khazen (till August) Srikanth Ramaswamy Rajnish Ranjan Michael Reimann Renaud Richardet Farhan Tauheed Anirudh Vij Interns Damien Drix Michael Hull Elizabeth Ottens Dmimitri Probst Anna Traussnig Matthew Perich Visiting Researcher Prof. Yun Wang Visiting Professor Prof. Karlheinz Wilhelm Meier

BMI - Brain Mind Institute

Administration Claire Devillers (CHUV) Christian Fauteux Catherine Hanriot Amanda Pingree

Visualization of the unifying model of a cortical column of a young rat. In false colors indicated are the different morphological types of cells.

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EPFL School of Life Sciences

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2011 Annual Report

Other SV Professors and Newcomer Professors

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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 Directors’ Group of EFPIA (European Federation of Pharmaceutical Industry Associations) and was the founding chairman of the

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

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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).

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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.

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EPFL School of Life Sciences - 2011 Annual Report

Rainer Group www.unifr.ch/inph/vclab

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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.

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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.

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Schorderet Group www.irovision.ch

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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

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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.

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Tanner

EPFL School of Life Sciences - 2011 Annual Report

http://www.swisstph.ch

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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

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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

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