Epfl SV Brain Mind Institute AR2012 by EPFL School of Life Sciences

EPFL School of Life Sciences - 2012 Annual Report

Table Of Contents

Preamble.....................................................................................................................................3 Highlights of 2012.......................................................................................................................6 Honors-Awards-Announcements.................................................................................................7 Undergraduate Studies.................................................................................................................8 Doctoral Programs.......................................................................................................................9 SV Doctoral Graduates..............................................................................................................10 SV Masters Graduates................................................................................................................12 School of Life Sciences at a Glance...........................................................................................13

Centers.............................................................................................................................14

Blue Brain Project......................................................................................................................14 Center for Biomedical Imaging Research....................................................................................16 Center for Neuroprosthetics ......................................................................................................18

BMI..................................................................................................................................21

Aebischer Lab............................................................................................................................22 Blanke Lab.................................................................................................................................24 Courtine Lab..............................................................................................................................26 Fraering Lab...............................................................................................................................28 Gerstner Lab..............................................................................................................................30 Herzog Lab................................................................................................................................32 Lashuel Lab...............................................................................................................................34 Magistretti Lab...........................................................................................................................36 Markram Lab.............................................................................................................................38 Moore Lab.................................................................................................................................40 Petersen Lab..............................................................................................................................42 Sandi Lab...................................................................................................................................44 Schneggenburger Lab................................................................................................................46

IBI....................................................................................................................................49

Auwerx - Schoonjans Lab..........................................................................................................50 Baekkeskov Lab.........................................................................................................................52 Barrandon Lab...........................................................................................................................54 Dal Peraro Lab...........................................................................................................................56 Deplancke Lab..........................................................................................................................58 Hubbell Lab...............................................................................................................................60 Jensen Lab.................................................................................................................................62 Lutolf Lab..................................................................................................................................64 Naef Lab....................................................................................................................................66 Swartz Lab.................................................................................................................................68 Wurm Lab.................................................................................................................................70

Co-affiliated Research Groups.........................................................................................72

Aminian Lab..............................................................................................................................72 Fantner Lab ...............................................................................................................................73 Guiducci Lab.............................................................................................................................74 Hatzimanikatis Lab....................................................................................................................75 Ijspeert Lab................................................................................................................................76 Johnsson Lab.............................................................................................................................77 Jolles-Haeberli Lab ...................................................................................................................78 Lacour Lab ................................................................................................................................79 Maerkl Lab ...............................................................................................................................80 Mermod Lab..............................................................................................................................81 Micera Lab ...............................................................................................................................82 Millán Lab ................................................................................................................................83 Pioletti Lab ...............................................................................................................................84

EPFL School of Life Sciences - 2012 Annual Report

Psaltis Lab .................................................................................................................................85 Radenovic Lab ..........................................................................................................................86 Renaud Lab ..............................................................................................................................87 Roke Lab ..................................................................................................................................88 Stergiopulos Lab .......................................................................................................................89 Van de Ville Lab ........................................................................................................................90 Van den Bergh Lab ...................................................................................................................91

GHI..................................................................................................................................93

Blokesch Lab.............................................................................................................................94 Cole Lab....................................................................................................................................96 Fellay Lab..................................................................................................................................98 Harris Lab................................................................................................................................100 Lemaitre Lab............................................................................................................................102 McKinney Lab.........................................................................................................................104 Trono Lab................................................................................................................................106 Van der Goot Lab....................................................................................................................108

ISREC.............................................................................................................................111

Aguet Lab................................................................................................................................112 Brisken Lab..............................................................................................................................114 Constam Lab............................................................................................................................116 De Palma Lab..........................................................................................................................118 Duboule Lab............................................................................................................................120 Gönczy Lab.............................................................................................................................122 Hanahan Lab...........................................................................................................................124 Hantschel Lab..........................................................................................................................126 Huelsken Lab ..........................................................................................................................128 Kühn Lab.................................................................................................................................130 Lingner Lab..............................................................................................................................132 Meylan Lab..............................................................................................................................134 Radtke Lab...............................................................................................................................136 Simanis Lab.............................................................................................................................138 Bucher Group..........................................................................................................................140

Other Professors............................................................................................................142

Knowles...................................................................................................................................142 Tanner - Swiss TPH..................................................................................................................143 Molinari Group........................................................................................................................144 Rainer Group...........................................................................................................................146 Schorderet Group....................................................................................................................148 Core Facilities & Technology Platforms.....................................................................................151 Bioelectron Microscopy...........................................................................................................152 BioImaging & Optics...............................................................................................................153 Bioinformatics & Biostatistics...................................................................................................154 Biomolecular Screening...........................................................................................................155 Flow Cytometry ......................................................................................................................156 Histology ................................................................................................................................157 Proteomics...............................................................................................................................158 Protein Crystallography............................................................................................................159 Protein Expression...................................................................................................................160 Transgenic ..............................................................................................................................161 Phenotyping Unit.....................................................................................................................162

Introduction

Core Facilities & Technology Platforms..........................................................................151

EPFL School of Life Sciences - 2012 Annual Report

Preamble The School of Life Sciences is organized to teach students at the interface of biology and engineering - indeed quantitative, analytical and design-oriented life scientists, whether pursuing a Bachelor of Science in Life Sciences and Technology, a Master of Science in Life Sciences and Technology or Bioengineering, or a Doctor of Philosophy in Molecular Life Sciences, Neurosciences, or Biotechnology and Bioengineering. The School’s professors come from diverse backgrounds in biology, chemistry, physics, engineering and medicine to bring their passion for developing new fundamental understanding of critical questions in the life sciences and translating that understanding toward impacting human health through engineering solutions. The School’s span from the fundamental to the translational incorporating both basic scientists and engineers positions it in a unique position for profound impact.

Jeffrey A. Hubbell - Dean of Life Sciences

Introduction

The situation within the School in 2012 is exciting. Our professors have been awarded a total of 18 ERC grants, reflecting the broad enthusiasm of the scientific community for our scientific performance. The Center for Neuroprosthetics, a collaboration with the School of Engineering, has been launched and is fully up to speed, including ongoing human clinical investigations. The Human Brain Project, led by professors in the Brain Mind Institute, is having broad impact in neuroscience in Europe and worldwide. The Swiss Institute for Experimental Cancer Research has launched a collaboration with the University of Lausanne and the Centre Hospitalier Universitaire Vaudoise to create the Swiss Cancer Center Lausanne, bringing together basic and translational scientists and engineers to solve fundamental problems in cancer biology and therapy. These and other strategic activities are exciting expressions of the enthusiasm and leadership roles of the professors of the School of Life Sciences.

EPFL School of Life Sciences - 2012 Annual Report

Highlights of 2012 February: Marc Moniatte, EPFL Proteomics Core Facility and INSERM-EPFL joint laboratory led by Christian Doerig joined forces with a team at Institut Pasteur (Paris) on an Antivalarial joint research project. http://actu.epfl.ch/news/ antimalarial-successful-joint-research/

March: The SV labs welcomed 17 enthusiastic high school students from all corners of Switzerland under the framework of La Science Appelle les Jeunes! (Schweizer Jugend forscht!) These students experienced lab work first-hand while completing and presenting a mini-project. http:// fr.sjf.ch/index.cfm

March : As a part of “Science, qui tourne.” , Denis Duboule (ISREC) and Jacques Neirynck, a national councilor, held a joint interview at the Rolex Learning Center on the subject of the future effect on society caused by low cost human DNA sequencing. http://actu.epfl.ch/news/low-cost-genome-decoding-for-better-or-for-worse-2/

EPFL Announces the Next Phase for its Center for Neuroprosthetics, (CNP) defining and establishing a truly interdisciplinary field of study merging neuroscience with engineering and medicine, and efficiently translating major breakthroughs from bioengineering and neuroscience into clinical settings. http://cnp.epfl.ch/

March: EPFL Prospective Students Days: The Life Sciences Teaching Section welcomed more than 200 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 December. More information : http://sv.epfl.ch/ prospective-students/march2012

Summer: The 2012 International Summer Research Program for undergraduate students hosted 25 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. http://sv.epfl.ch/summer-research

August: The annual Life Sciences Symposium was hosted by GHI, on the theme “Global Health meets Infection Biology” with a topnotch roster of speakers. The symposium as usual was a resounding success. During the symposium, the 2012 Debiopharm Life Sciences Award was given to Professor Daniel D. Pinschewer (University of Geneva) and Doctors Daan Noordermeer (EPFL) and Kelly Tan (University of Geneva) each received a Junior Debiopharm Group™ Life Sciences Award. http://actu.epfl.ch/news/three-scientiﬁc-prizes-awarded-by-debiopharm/

For more information and up-to-date SV news:

http://actu.epfl.ch/search/sv/

EPFL School of Life Sciences - 2012 Annual Report

Honors-Awards-Announcements Dimitri Van De Ville (IBI - STI) - Pfizer Award

Olaia Naveiras (IBI) - Jose Carreras Junior Investigator

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Career Fellowship

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Denis Duboule (ISREC) - New member of the British Royal Society.

Nicola Harris (GHI) and Felix Naef (IBI) - 2012 Leenaards

Swiss Final, Zurich.

Hilal Lashuel (BMI) - World Economic Forum Honoree

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Switzerland participants, CERN, Geneva. Muralidhar -

Shruti Muralidhar (BMI) & Adrian Ranga (IBI) - FameLab

Foundation Scientific Prize

QGel (start-up) - IBI co-founders: Matthias Lutolf and Jeff

Kai Johnsson (IBI-SB) – new member of the EMBO-

Hubbell - PERL Prizes

European Molecular Biology Organization.

Denis Duboule (ISREC) - US National Academy election.

QGel (start-up) - IBI co-founders: Matthias Lutolf and Jeff

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Hubbell - Vigier Prizes

Daan

Noordermeer

(ISREC)

Junior

Douglas Hanahan (ISREC) - 2012 Award for Cancer

Debiopharm

Research from the Fondazione San Salvatore, Lugano, CH

Group™ Prize

Melanie Blokesch (GHI), Nicola Harris (GHI), Jeffrey Melody Swartz (GHI)

Jensen (IBI), and Matthias Lutolf (IBI) European Research

- 2012 MacArthur Foundation

Council (ERC) Starting Grants

A ug

Fellow

Bart Deplancke (IBI) Prix SSV- Ambition Wulfram Gerstner (BMI) Prix SSV – Education

Jacques Fellay (GHI) - National Latsis Prize

Gisou van der Goot (GHI) - Prix Polysphère d-Or

Melanie Blokesch (GHI) - Best Teaching Evaluation prize

Olaf Blanke (BMI) - Cloëtta Foundation Prize

Introduction

Friedemann Zenken (BMI) - Teaching Assistant IC Award

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Swiss League Against Cancer

Joerg Huelsken (ISREC) - Robert Wenner Prize by the

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Ambition prize

Bart Deplancke (IBI) and Sebastian Maerkl (IBI - STI) -

EPFL School of Life Sciences - 2012 Annual Report

Undergraduate Studies 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 specializations. Among these are Neurosciences and Neuroengineering, Molecular Medicine and System Biology. Each specialization is made up of 19 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 Biocomputing and Computational Neurosciences. 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), Biocomputing (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. Bertrand Rey - photographer

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/

EPFL School of Life Sciences - 2012 Annual Report

Doctoral Programs 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 during our Hiring Days which occurs twice a year, the end of January and the end of June. Hiring Days last two and a half days: one-half day of general information followed by two days of lab immersion and evaluation.

Neuroscience (EDNE) provides its stu-

dents 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

Biotechnology and Bioengineering (EDBB) prepares doctoral students

to become leaders in the fast-growing academic and industrial biotechnology and bioengineering sectors by providing a depth of knowledge and competence in their specific research areas as well as a breadth of knowledge in biology, bioengineering, and biotechnology. Focus areas include: biomolecular engineering and biomaterials; cell, tissue, and process engineering; stem cell biotechnology; orthopaedic engineering; microtechnology and nanotechnology; biomechanics and mechanobiology; molecular and cellular biophysics; computational biology; genomics and proteomics; advanced biomedical imaging and image processing. http:// phd.epfl.ch/edbb

Molecular Life Sciences (EDMS) aims at providing doctoral students with the education necessary to become leaders in biological research, implementing the latest state of the art. The combination of laboratory based research with access to modern technological platforms, coursework, in-house seminars, national and international conferences, etc., forms the basis of this education. The programâ&#x20AC;&#x2122;s themes include cell biology, developmental biology, biochemistry & biophysics, molecular genetics, cancer research, microbiology, host-pathogen interactions, immunology, systems biology, computational biology, human genetics, stem cells and metabolism. The EDMS PhD program offers exciting PhD positions to talented and ambitious young researchers.

Introduction

http://phd.epfl.ch/edmshttp://phd.epfl.ch/edms

EPFL School of Life Sciences - 2012 Annual Report

SV Doctoral Graduates

Introduction

EPFL School of Life Sciences - 2012 Annual Report

SV Masters Graduates Master Bioengineering Graduates 2012

Master Life Sciences & Technology Graduates 2012

EPFL School of Life Sciences - 2012 Annual Report

Introduction

School of Life Sciences at a Glance

Centers

EPFL School of Life Sciences - 2012 Annual Report

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

Director: Prof. Henry Markram Introduction

The ultimate goal of the Blue Brain Project is to reverse engineer the mammalian brain by iteratively reconstructing models using biological data and principles and building on predictions generated. To achieve this goal the project has set itself four key objectives: • Create a generic Brain Simulation Facility with the ability to reconstruct brain models of the healthy and diseased brain, at different scales, with different levels of detail for different species. • Demonstrate the feasibility and value of this strategy by creating and validating a biologically detailed model of the neocortical column in the somatosensory cortex of young rats. • Use this model to refine the basic strategy to reconstruct brain models using biological data and principles and determine the extent to which new design insights can be predicted. • Exploit these validated and predicted principles to create larger more detailed brain models, and to develop strategies to eventually reconstruct the complete human brain using.

Keywords

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

Description of BBP activities & results 2012

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 eighth 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. The first version of the unifying model of the neocortical column was completed in 2008 and presented at the FENS meeting by the Blue Brain Project. The BBP integrated (and continually integrates) vast amounts of biological data on the rat neocortex and uses this reservoir of reconciled data to generate a continuously updated model, which is then simulated on Blue Brain Simulation Platform. The results were showcased during a presidential lecture at the Forum for European Neuroscience (FENS, Barcelona) and discussed with the scientific community at the largest annual convention of neuroscientists (Neuroscience, New Orleans), where 20 coordinated scientific posters were presented to detail the development and refinement of the cortical column unifying model.

Several insights from this first unifying model have been published in high impact journal publications and the full publication and release of the model are foreseen for 2013. Technical advances to the platform have been published at competitive conferences and a keynote lecture at the major supercomputing conference (Supercomputing, Salt Lake City) have been given. A notable insight from the model (published in PNAS 2012) is that the locations of synapses (the local connectome) between neurons can be accurately predicted using the reconstruction algorithms developed. Through the reconstruction the column, the BBP was able to identify key principles that determine synapse-scale connectivity by comparing the reconstructed circuit to a mammalian sample. Using these principles, it has become possible to accurately predict synapse location with 75-95% accuracy . Additionally, a systemic simplification strategy for the detailed model of the neocortical column was developed, which allows BBP to develop progressively abstract (simpler) models such that it is possible to focus on a particular aspect or function. Another scientific focus of the BBP in 2012 was to drive and coordinate the preparation of the Human Brain Project (HBP) proposal, selected as a FET Flagship initiative of the European Commission in 2013. This enormous effort involved numerous BBP scientists and managers as well as 150 scientific groups in various parts of the world. The preparatory phase project HBP-PS was successfully completed in April 2012 and a publically available report was created and disseminated. The HBP, involving initially 87 partner institutions, will be coordinated by EPFL and have a budget of one billion euros to deliver 10 years of world-beating science at the crossroads of science and technology. This success, essentially the largest research grant in EU funding history, represents a huge success for the EPFL and the ETH Board, who have backed the project during its preparation, and Swiss science in general. Following the mandate of the ETH Board, substantial efforts also went into the preparation of Blue Brain in the form of a national research infrastructure from 2013 onwards. Most notably, this includes the technical and infrastructural preparation for a future opening of certain Blue Brain assets to a larger group of scientists. This work will intensify in 2013 and lead to the release of a first web-based portal allowing scientists to use the Blue Brain Simulation Platform. Lastly, the Blue Brain Project succeeded in securing important international collaborations such as a strategic alliance between the King Abdullah University of Science and Technology (KAUST) and EPFL/BBP on neuro-inspired high performance computing and a participation in the Helmholtz Portfolio Grant allowing future collaboration with important computing centers in Germany.

EPFL School of Life Sciences - 2012 Annual Report

Team Members

Selected Publications

S.L.Hill, Y.Wang, I.Riachi, F.Schürmann, H.Markram: Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits, PNAS, 2012 Oct 16;109(42):E2885-94. doi: 10.1073/ pnas.1202128109. Epub 2012 Sep 18. S.Druckmann, S.Hill, F.Schürmann, H.Markram, I.Segev: A Hierarchical Structure of Cortical Interneuron Electrical Diversity Revealed by Automated Statistical Analysis, Cerebral Cortex, Cereb. Cortex (2012), doi: 10.1093/cercor/bhs290. A.Gidon and I.Segev: Principles governing the operation of synaptic inhibition in dendrites, Neuron, 2012 Jul 26;75(2):330-41. G.Khazen, S.L.Hill, F.Schürmann, and H.Markram: Combinatorial Expression Rules of Ion Channel Genes in Juvenile Rat (Rattus norvegicus) Neocortical Neurons, PLoS One, 7(4): e34786. doi:10.1371/journal.pone.0034786. S.Lasserre, J.Hernando, S.Hill, F.Schürmann, P. de Miguel Anasagasti, G.Abou Jaoudé, H.Markram: A Neuron Mesh Representation for Visualization of Electrophysiological Simulations, IEEE Transactions on Visualization and Computer Graphics, 18 (2): p. 214-217. S.Ramaswamy, S.L.Hill, J.G.King, F.Schürmann, Y.Wang, and H.Markram: 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. F.Tauheed, T.Heinis, F.Schürmann, H.Markram, A.Ailamaki: SCOUT: Prefetching of Latent Structure Following Queries, VLDB 2012 S.Eilemann, A.Bilgili, M.Abdellah, J.Hernando, M.Makhinya, R.Pajarola, and F.Schürmann: Parallel Rendering on Hybrid Multi-GPU Clusters, EGPGV 2012 J. Hernando, F.Schürmann, L.Pastor (2012), Towards real-time visualization of detailed neural tissue models: view frustum culling for parallel rendering, BioVis 2012 1Tauheed F, Biveinis L, Heinis T, Schürmann F, Markram H, Ailamaki A. Accelerating range queries for brain simulations, Proceedings of the 28th International Conference on Data Engineering (2012), pp. 941-952

General Project Manager Felix Schürmann Project Managers Buncic Nenad Fabien Delalondre Marc-Oliver Gewaltig Sean Hill Eilif Muller Julian Shillcock Stefan Eilemann Senior Science Writer Richard Walker Operations Alejandro Schiliuk Postdoctoral Fellows Guy Antoine Atenekeng Ahmet Bilgili Joe Graham Juan Hernando Daniel Keller Srikanth Ramaswamy Rajnish Ranjan Martin Telefont Benjamin Torben-Nielsen Werner Van Geit Thomas Heinis Research Assistant Melissa Cochrane

Engineers Carlos Aguado Sanchez Athanassia Chalimoudra Jean-Denis Courcol Valentin Haenel James Gonzalo King Bruno Ricardo Magalhaes Daniel Nachbaur Jeff Muller Stefano Zaninetta Sandro Wenzel PhD Students Marwan Abd Ellah Guiseppe Chindemi Lida Kanari Michael Reimann Renaud Richardet Farhan Tauheed Anirudh Vij Rahul Valiya Veettil Willem Wybo Interns Jafet Villafranca Diaz Ronny Hatteland Dan Ibanez Amine Achkar Kay G Hartmann Drew P Minnear Sarah Strauss Berat Denizdurduran Bidur Bohara Visiting Researcher Yun Wang Visiting Professors Karlheinz Wilhelm Meier Michael Hines Administration Christian Fauteux Catherine Hanriot Amanda Pingree Daphne Rondelli

of selected touch between neurons.

locations

Centers

Illustration

EPFL School of Life Sciences - 2012 Annual Report

Center for Biomedical Imaging Research http://www.cibm.ch/

Director: Prof. Rolf Gruetter

From Mouse to Patient History of the Center

The CIBM is the result of a major research and teaching initiative of the partners in the Science-Vie-Societe (SVS) project, i.e. Ecole Polytechnique Federale de Lausanne (EPFL), Universite de Lausanne (UNIL), Universite de Geneve (UNIGE), Hopitaux Universitaire Geneve (HUG), Centre Hospitalier Universitaire Vaudois Lausanne (CHUV), founded with generous support from the Fondations Jeantet and Leenaards. The CIBM was designed an imaging research center, committed to conducting biomedical imaging research in the context of biomedical research questions of importance, with the overall aim to bring together as equals imaging scientists and biomedical researchers. The Center is comprised of seven Research Cores focused on specialized research support and technology development and is active on three main sites at the EPFL, CHUV and HUG.

2012 Highlights • 115 publications • 1 starting ERC grant

Mission and Aim

The CIBMseeks to advance our understanding of biomedical processes in health and disease, focusing on mechanisms of normal functioning, pathogenic mechanisms, characterization of disease onset prior to structural damage, metabolic and functional consequences of gene expression, and non-invasive insights into disease processes under treatment. The research uses model systems ranging from transgenic animals to human subjects (“from mouse to man”) and fosters multi-disciplinary collaboration between basic science, biomedical science and clinical applications. The goal is to advance biomedical imaging, i.e. functional and metabolic imaging, while addressing biomedical questions of importance at the same time. This is accomplished by establishing a research network in imaging science to enhance biomedical research capabilities of the founding institutions and beyond, as well as within the CIBM.

Contact

To establish research projects, feel free to contact the Core director concerned (see below or www.cibm.ch) or info@ cibm.ch and we will be delighted to assist you.

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EPFL School of Life Sciences - 2012 Annual Report

Structure and Scope CIBM: 1 Center, 3 Sites, 5 Institutions, 7 Research Cores

Signal Processing and Image analysis core (M. Unser): The infrastructure includes multiple servers for data storage and processing. The aim is to perform high-level research in medical image analysis and develop theoretical foundations for new algorithms and mathematical tools for imaging addressing the need for advanced signal processing with large datasets being acquired, and complex questions to be answered. Phase Contrast Radiology core (G. Margaritondo): Ultra-high spatial and temporal resolution using using the TOMCAT beamline of the high quality swiss light source at the PSI in Villigen. The aim is to reach isotropic resolutions at the submicron scale within milliseconds and to develop novel approaches for phase-contrast radiology using conventional, laboratory-based sources. PET core (O. Ratib): A micro PET scanner linked to advanced radiochemistry research at the HUG, as well as a scanner at EPFL. The aim is to provide “conventional” imaging capabilities for the immediate evaluation of novel radiotracers, another is to focus on the synergies provided with combined studies on MR, including innovative mechanism for image registration.

Clinical Research Satellite at the HUG (F. Lazeyras): Clinical 3 Tesla TIM Trio scanner, 50% dedicated to clinical research and 50% to clinical service, with a complete accessary of functional-MRI equipment up to simultaneous EEG and MRI acquisition. A minimally invasive abdominal tumor ablation HiFU platform is operational. The aim is to develop and maintain state of the art MRI capabilities relevant for clinical research focusing on cognitive (dys)function and recovery in humans, as well as brain development. Clinical Research Satellite at the CHUV (M. Stuber): Clinical 3 Tesla TIM Trio scanner, 50% dedicated to clinical research and 50% to clinical service. A 32-channel cardiac coil and a 4-element carotid coil are available for cardiovascular research together with numerous high-end coils for neuro applications. The aim is to advance research and discovery through a better fundamental understanding of biological processes through advanced methods development enabling a direct translation from the bench to the bedside. Animal Imaging and Technology core (R. Gruetter): Ultra-high field MR equipment (100% research) • human 7 Tesla (1st actively shielded) • rodent 14 Tesla (world’s first) • rodent 9.4 Tesla The short bore of the 7 Tesla magnet makes it particularly suited for clinical studies and novel interventions, supported by a room for accommodating patients/volunteers. To minimize stress due to transport from the collaborating labs, a small on-site animal holding facility is present. Complemented with an RF laboratory and physiology support laboratories. The aim is to develop magnetic resonance imaging and spectroscopy capabilities in the context of specific biomedical research questions for animal imaging in rodents (primarily rats and mice) and for human brain imaging at very high magnetic fields. For more information see http://www.cibm.ch/page-60484-en.html.

A selection of images from all seven research cores.

Centers

EEG Brain Mapping core (C. Michel): State-of-the-art high density (MRI-compatible) EEG in- stallations at the university hospital in Geneva (HUG), the university medical school in Geneva (CMU), and at the university hospital in Lausanne (CHUV). The aim is to provide recording and analysis tools that allow studying the spatiotemporal dynamics of large-scale networks.

EPFL School of Life Sciences - 2012 Annual Report

Center for Neuroprosthetics http://cnp.epfl.ch/

Director: Prof. Olaf Blanke

Introduction

The Center for Neuroprosthetics (CNP) capitalizes on its unique access to advanced technologies and state of the art brain research present on the EPFL campus. Its aim is to develop new technologies that could support, repair and replace functions of the nervous system. The development of such technologies or devices, called neuroprostheses, requires a fundamental understanding of the neurobiological mechanisms of the functions that should be replaced or repaired, for example sensory perception, cognitive operations or the generation of motor commands. It also requires technological capabilities to design novel devices, to record and process signals and to translate them into control signals that can commend artificial limbs, bodies and robots, for motor function, or produce signals to activate the brain, in the case of sensory prostheses. The impact of neuroprosthetics for the treatment of sensory loss and impaired mobility has already been demonstrated. Over 200,000 people with impaired hearing have received cochlear implants and over 80,000 patients suffering from Parkinson’s disease and other neurological movement disorders have been treated with deep brain stimulation. With approximately a third of the population in Europe and the US afflicted by brain disorders, breakthroughs in cognitive neuroprosthetics will be necessary for treating patients suffering from cognitive deficits such as those caused by Alzheimer’s disease and vascular stroke.

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The Center for Neuroprosthetics is part of both the School of Engineering and the School of Life Sciences. It draws upon the EPFL’s expertise in biology, neuroscience, brain imaging, and genetics as well as biomedical, electrical, mechanical engineering, and nanotechnology. The Center will also draw upon EPFL’s cutting edge research in signal analysis, theoretical and computational neuroscience, the recently launched European Flagship “Human Brain Project” and the Swiss National Center of Competence in Research in “Robotics”. In addition, through support from the Bertarelli foundation, a new research collaboration - dedicated to translational neuroscience and neuroengineering - has been created between Harvard Medical School, EPFL’s Institute of Bio-engineering, and the Center for Neuroprosthetics. The Center for Neuroprosthetics is currently developing strategic partnerships with Geneva University Hospital (Hôpitaux Universitaires de Genève, HUG), Lausanne University Hospital (Centre Hospitalier Universitaire Vaudois, CHUV), and a major Swiss Rehabilitation Clinic (Clinique Romande de Réadaptation, CRR in Sion), as well as with the regional biomedical industry.

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EPFL School of Life Sciences - 2012 Annual Report

Four key projects define the core activities of the center: Walk again Restoring sensorimotor functions after spinal cord injury Intentions of a paralyzed rodent with spinal cord injury are decoded from real-time recording of brain activity. Decoded information is directly fed into a brain-spinal interface that computes optimal spinal cord stimulation patterns to execute the desired movement. As a result the animal is capable of locomotion and obstacle avoidance, even though the spinal cord motoneurons are physically separated from the brain. Bionic hand Restoring sensory and motor functions after arm or hand amputation Biocompatible flexible electrodes are implanted into different peripheral arm nerves of amputee patients. Movement commands of the amputee patient are decoded from signals in the implanted electrodes and transmitted to the prosthetic hand, where they are translated into movements of the prosthetic hand and fingers. Signals from different sensors in the prosthetic hand can also be transmitted via the implanted electrodes to the peripheral nerve to enable sensory functions such as the sense of touch and of finger position.

Rehabilitation of upper limb sensorimotor loss Providing neuro-technological tools for vascular stroke rehabilitation Merging insights from robotics and neuroengineering, our devices enable novel neurorehabilitation training for patients suffering from sensorimotor loss of the upper extremity. These tools are complemented by techniques from brain computer interfaces and virtual reality to further enhance rehabilitation outcomes for patients with sensorimotor loss, but also for patients suffering from chronic pain or cognitive deficits. Human-Computer confluence Decoding brain activity for feeling and moving artificial bodies and robots With robust real-time movement control of wearable devices and robots and with pioneering work in brain-machine interface and cognitive neuroscience, novel interaction paradigms are provided for mobility restoration, communication, neuroscience research, and entertainment.

Selected Publications:

Courtine G, Micera S, DiGiovanna J and MillĂĄn JdR (2013). Brain-machine interface: closer to therapeutic reality? The Lancet 381:515-7. Van den Brand R, Heutschi J, Barraud Q, DiGiovanna J, Bartholdi K, Huerlimann M, Friedli L, Vollenweider I, Moraud EM, Duis S, Dominici N, Micera S, Musienko P, Courtine G (2012). Restoring voluntary control of locomotion after paralyzing spinal cord injury. Science 336(6085):1182-5. Blanke O Multisensory brain mechanisms of bodily self-consciousness (2012). Nat Rev Neurosci 13(8):556-571. Dominici N, Keller U, Vallery H, Friedli L, van den Brand R, Starkey ML, Musienko P, Riener R, Courtine G (2012). Novel robotic interface to evaluate, enable, and train locomotion and balance after neuromotor disorders. Nature Medicine 18:1142-7. Panarese A, Colombo R, Sterpi I, Pisano F, Micera S (2012). Tracking motor improvement at the subtask level during robot-aided neurorehabilitation of stroke patients. Neurorehabil Neural Repair 26(7):822-33. Tombini M, Rigosa J, Zappasodi F, Porcaro C, Citi L, Carpaneto J, Rossini PM, Micera S (2012). Combined analysis of cortical (EEG) and nerve stump signals improves robotic hand control. Neurorehabil Neural Repair 26(3):275-81. Delivopoulos E, Chew D, Minev IR, Fawcett JW, Lacour SP (2012). Concurrent recordings of bladder afferents from multiple nerves using a microfabricated PDMS microchannel electrode array. Lab on Chip 12:2540-2551. Huang YY, Terentjev E, Oppenheim T, Lacour SP, Welland ME (2012). Fabrication and electromechanical characterization of near-field electrospun composite fibers. Nanotechnology 23:105305. Tzovara A, Murray M, Bourdaud N, Chavarriaga R, MillĂĄn JdR and De Lucia M (2012). The timing of exploratory decision-making revealed by single-trial topographic EEG analyses. Neuroimage 4:1959-69.

Centers

Ionta S, Heydrich L, Lenggenhager B, Mouthon M, Fornari E, Chapuis D, Gassert R, Blanke O (2011). Multisensory mechanisms in temporo-parietal cortex support self-location and first-person perspective. Neuron 70(2):363-74.

EPFL School of Life Sciences - 2012 Annual Report

BMI

Brain Mind Institute

Sandi Carmen - Director

The mission of the Brain Mind Institute is to understand the fundamental principles of brain function in health and disease, by 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. Research at the BMI focuses on four main areas: • Molecular neurobiology and mechanisms of brain function and dysfunction, with a particular focus on neurodegeneration and stress-related psychopathologies. • Molecular and cellular mechanisms of synapse and microcircuit function up to the behavioral level and including metabolic aspects. • Sensory and body perception and cognition in humans. • Designing innovative interventions to restore sensorimotor functions after neural disorders.

BMI - Brain Mind Institute

In all areas, the BMI strives to integrate knowledge gained by multidisciplinary approaches and across different disciplines and research laboratories. An important second mission of the BMI is to bridge scientific approaches and questions with research carried out in the EPFL campus, as well as in related institutions and companies in the area, specifically with the fields of nano- and micro-technology, computer sciences, physics, neuroprosthetics, robotics, signal and medical imaging processing, genetics, psychiatry and neurology. Major goals of the BMI are to bridge basic science approaches with clinical applications and to merge areas of experimental work with theory and modeling. Finally, the BMI is fully engaged in the teaching mission of the School of Life Sciences at the Bachelor and Master levels (with a full Neuroscience track at the Master level) and organizes the PhD program in Neurosciences.

EPFL School of Life Sciences - 2012 Annual Report

Aebischer Lab http://len.epfl.ch/

Patrick Aebischer was trained as an MD (1980) and a Neuroscientist (1983) at the Universities of Geneva and Fribourg in Switzerland. Until 1992, he worked as Faculty member at Brown University in Providence (USA), where he became Chairman of the Section of Artificial Organs, Biomaterials and Cellular Technology in 1991. He returned to Switzerland in 1992, as Professor and Director of the Surgical Research Division and Gene Therapy Center at the Centre Hospitalier Universitaire Vaudois in Lausanne. Since 2000, Patrick Aebischer is President of EPFL. 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 including Parkinson’s disease, Amyotrophic Lateral Sclerosis and Alzheimer’s disease, as well as in designing innovative treatments to slow down the progression of neuronal degeneration. We develop new technologies for animal modeling of these devastating pathologies and comprehensive analysis of the degenerative process. Preclinical studies in animal models are designed to investigate gene therapies as a novel approach to treat neurodegenerative disorders.

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 2012

With the recent discovery of genes implicated in familial forms of neurodegenerative diseases, our understanding of the pathogenesis has vastly improved. However, it is critical to design effective animal models to investigate how the disease process affects neuronal survival and, most importantly, brain functions. In the context of Parkinson’s disease, our lab has been involved in designing an animal model based on the expression of pathogenic proteins including α-synuclein in the basal ganglia. 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 (Gaugler et al., 2012). In addition, these functional defects are linked to impairments in the secretory pathway of the diseased neurons (Coune et al., 2011). We are currently investigating how genetic determinants of aging, the main risk factor for Parkinson’s disease, modify α-synuclein pathology. In particular, we found that PGC-1alpha, a transcriptional co-regulator implicated in the control of the mitochondrial function, has a major role in the survival of nigral dopaminergic neurons, a population of neurons which

is selectively vulnerable to Parkinson’s disease (Ciron et al., 2012). Along these lines, our lab has pursued the development of animal models of the Alzheimer’s pathology using the viral vector technology. In particular, we have developed AAV vectors expressing tau and the amyloid precursor protein, which proved effective at replicating cardinal features of the disease, such as amyloid plaques and hyperphosphorylated tau tangles in neurons of the mouse frontal cortex. We found that the tau pathology led to prominent neurodegeneration and brain dysfunction as demonstrated by behavioural tests. In the past two years, we have explored advanced imaging approaches to assess the changes in the abundance of metabolites in animal by NMR spectroscopy (in collaboration with R. Gruetter; Mlynarik et al., 2012, Coune P et al, 2013), as well as the deposition of amyloid plaques in whole brain by X-ray coherent tomography (in collaboration with the Paul Scherrer Institute; Pinzer et al., 2012). These studies highlight state-of-the-art techniques to quantitatively assess early pathological signatures of neurodegeneration, in representative animal models of Parkinson’s and Alzheimer’s disease. Our laboratory is dedicated to the development of gene therapy systems for the treatment of motor neuron diseases including amyotrophic lateral sclerosis and spinal muscular atrophy. We focus on adeno-associated vectors, which are currently considered as the most effective vector to target post-mitotic cells inside the CNS. Our goal is to tackle the identified cause of disease, such as the gain of toxic function for mutated human SOD1, or the loss of SMN function that lead to motor neuron degeneration. Using relevant animal models of disease, we work on establishing the proof-of-principle of gene therapy based on stringent criteria for systemic efficacy, and explore how to up-scale these techniques from rodent to primate species (Towne et al., 2011).

EPFL School of Life Sciences - 2012 Annual Report

Selected publications

Pinzer BR, Cacquevel M, Modregger P, McDonald SA, Bensadoun JC, Thuering T, Aebischer P, Stampanoni M. (2012) Imaging brain amyloid deposition using grating-based differential phase contrast tomography. Neuroimage, 16;61(4):1336-46. Gaugler MN, Genc O, Bobela W, Mohanna S, Ardah MT, El-Agnaf OM, Cantoni M, Bensadoun JC, Schneggenburger R, Knott GW, Aebischer P, Schneider BL. (2012) Nigrostriatal overabundance of α-synuclein leads to decreased vesicle density and deficits in dopamine release that correlate with reduced motor activity. Acta Neuropathol.,123(5):653-69 Aebischer P. (2012) Philanthropy: The price of charity. Nature, 481:260 Ciron C., Lengacher S., Dusonchet J., Aebischer P., Schneider B.L. (2012) Sustained expression of PGC-1α in the rat nigrostriatal system selectively impairs dopaminergic function, Hum Mol Genet., 21:1861-76 Coune P.G., Bensadoun J.C., Aebischer P., Schneider B.L. (2011) Rab1A OverExpression 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 Marroquin Belaunzaran O., Campana C., Cordero M.I., Setola V., Bianchi S., Galli C., Bouche N., Mlynarik V., Gruetter R., Sandi C., Bensadoun J.C., Molinari M., Aebischer P. (2011) Chronic Delivery of Antibody Fragments Using Immunoisolated Cell Implants as a Passive Vaccination Tool. Plos One, 6:e18268, Dusonchet J., Kochubey O., Stafa K., Young S.M. Jr., Zufferey R., Moore D.J., Schneider B.L., Aebischer P. (2011) A rat model of progressive nigral neurodegeneration induced by the Parkinson’s disease-associated G2019S mutation in LRRK2. J Neurosci., 31:907-12

Team Members Research Associate Bernard Schneider

Postdoctoral Fellows Julianne Aebischer Matthias Cacquevel Carine Ciron David Genoux Karin Löw PhD students Wojciech Bobela Elisabeth Dirren Aurélien Lathuilière Cylia Rochat Lu Zheng Technicians Aline Aebi Philippe Colin Fabienne Pidoux Vivianne Padrun Christel Sadeghi Julien Barroche Sandrine Faustino Pinheiro Visiting Students Nathalie Bossanne Patrick Chirdon (Fulbright) Smitha Sarma Maria Zamfir Administrative Assistant Ursula Zwahlen

BMI - Brain Mind Institute

Towne C., Setola V., Schneider B.L., Aebischer P. (2011) 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

AAV vectors injected in the lateral ventricle of mouse neonates transduce motoneurons (stained for ChAT) and astrocytes (stained for GFAP) in the lumbar spinal cord. We compare GFP expression induced by AAV6-cmv (in motoneurons, left panel) with AAV9-gfaABC1D (in astrocytes, right panel).

EPFL School of Life Sciences - 2012 Annual Report

Blanke Lab http://lnco.epfl.ch/ Olaf Blanke is director of the Center for Neuroprosthetics at the Ecole Polytechnique FĂŠdĂŠrale de Lausanne (EPFL), holds the Bertarelli Foundation Chair in Cognitive Neuroprosthetics, and is Professor of Neurology at the Department of Clinical Neurosciences at Geneva University Hospital. In his research, he applies paradigms from cognitive science, neuroscience, neuroimaging, robotics, and virtual reality in healthy subjects and neurological patients 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 neuroprosthetics and neurorehabilitation.

Olaf Blanke Full Professor

Introduction

The Laboratory of Cognitive Neuroscience targets the brain mechanisms of body perception, body awareness and selfconsciousness. Projects rely on the investigation of healthy subjects and neurological patients by combining psychophysical and cognitive paradigms, state of the art neuroimaging techniques (fMRI, intracranial and surface EEG), and engineering-based approaches (virtual reality, vestibular stimulation, and robotic devices). Next to studying the brain mechanisms of body perception, cognition, and selfconsciousness, we actively pursue research in neuroprosthetics, neurorehabilitation and in interdisciplinary fields of virtual reality, neuroscience robotics, presence research, and brain-computer interfaces.

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.

Zwaag et al., 2012). This method allowed us to define several distinct representations of each individual finger in the cortex and the cerebellum. Ongoing work extends these findings to the understanding of how these representations are altered in cases of phantom limb pain in amputee patients and patients suffering from paraplegia due to spinal cord injury. In 2012 we also developed a novel system that integrates the technologies of virtual reality (VR) and brain computer interfaces (BCI) with cognitive neuroscience. Using automatize stimulation we induced ownership for virtual hands at unprecedented levels and described the electrophysiological brain mechanisms (Evans & Blanke, 2013). Additionally, the study showed that the experimentallyinduced extension of ownership to virtual hands recruits highly similar brain mechanisms in fronto-parietal cortex as does motor imagery based BCI. We currently extend this knowledge to VR- and BCI-based neuroprosthetics translating these insights to patients with limb amputation and limb paralysis following vascular stroke.

Results Obtained in 2012

One of the major developments and results achieved in 2012 was the description of a method for mapping individual finger representation in the somatosensory cortex of the brain and of the cerebellum, using ultra-high field magnetic resonance imaging (Martuzzi et al., 2012; van der

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Blanke O. Multisensory brain mechanisms of bodily self-consciousness (2012). Nat Rev Neurosci. 13(8):556-571. Aspell JE, Palluel E, Blanke O (2012b). Early and late activity in somatosensory cortex reflects changes in bodily self-consciousness: an evoked potential study. Neuroscience. 216:110-122. Evans N, Blanke O (2013). Shared electrophysiology mechanisms of body ownership and motor imagery. Neuroimage. 64:216-228. Ionta S, Sforza A, Funato M, Blanke O (2013). Anatomically plausible illusory posture affects mental rotation of body parts. Cogn Affect Behav Neurosci. 13(1):197-209. Kannape OA, Blanke O (2012). Agency, gait and self-consciousness. Int J Psychophysiol. 83(2):191-199. Lopez C, Blanke O, Mast FW (2012). The human vestibular cortex revealed by coordinate-based activation likelihood estimation meta-analysis. Neuroscience. 212:159-179. Martuzzi R, van der Zwaag W, Farthouat J, Gruetter R, Blanke O (2012). Human finger somatotopy in areas 3b, 1, and 2: A 7T fMRI study using a natural stimulus. Hum Brain Mapp. doi: 10.1002/hbm.22172. Prsa M, Gale S, Blanke O (2012). Self-motion leads to mandatory cue fusion across sensory modalities. J Neurophysiol. 108(8):2282-2291.

Team Members Postdoctoral Fellows Kanayama Noriaki Llobera Mahy Joan Martuzzi Roberto Salomon Roy Prsa Mario Palluel Estelle Herbelin Bruno Ionta Silvio Serino Andrea Van Elk Michiel Brooks Anna

PhD students Akselrod Michel Berger Steve Michel Evans Nathan Forget Joachim Gale Steven Jimenez Rezende Danilo Marchesotti Silvia Pasqualini Isabella Pfeiffer Christian Kaliuzhna Mariia Pozeg Polona Rognini Giulio Sengul Ali Romano Daniele Peer Michael

Sengül A, van Elk M, Rognini G, Aspell JE, Bleuler H, Blanke O (2012). Extending the body to virtual tools using a robotic surgical interface: evidence from the crossmodal congruency task. PLoS One. 7(12):e49473.

Master students Macku Petr Noel Jean-Paul Visciòla Ludovica Tsimpanouli Maria-Efstratia

van der Zwaag W, Kusters R, Magill A, Gruetter R, Martuzzi R, Blanke O, Marques JP (2012). Digit somatotopy in the human cerebellum: A 7T fMRI study. Neuroimage, 67(C):354-62.

Administrative Assistant Gordana Kokorus

van Elk M, Blanke O (2012). Balancing bistable perception during self-motion. Exp. Brain. Res., 222(3):219-228. Ionta S., Heydrich L., Lenggenhager B., Mouthon M., Fornari E, Chapuis D., Gassert R., Blanke O. (2011). Multisensory mechanisms in temporo-parietal cortex support self-location and first-person perspective. Neuron, 70(2):363-74. Lopez C., Mercier M. R., Halje P. and Blanke O. (2011). Spatiotemporal dynamics of visual vertical judgments: early and late brain mechanisms as revealed by high-density electrical neuroimaging. Neuroscience, 181:134-49.

BMI - Brain Mind Institute

Lenggenhager B., Halje P. and Blanke O. (2011). Alpha band oscillations correlate with illusory self-location induced by virtual reality. European Journal of Neuroscience, 33(10):1935-43.

Schematic representation of the finger maps within the primary somatosensory area, as obtained using ultra-high field fMRI.

EPFL School of Life Sciences - 2012 Annual Report

Courtine Lab

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

Even though Grégoire Courtine was trained in Mathematics and Physics, he received his PhD in Experimental Medicine from the Inserm Plasticity and Repair, France, in 2003. After a Post-doctoral training at Los Angeles (UCLA), he established his own laboratory at the University of Zurich in 2008. In Dec 2011, he accepted the International paraplegic foundation (IRP) chair in spinal cord repair in the center for neuroprosthetics at the EPFL. He has received numerous honors such as the UCLA Chancellor’s award, the Schellenberg Prize for his advances in spinal cord repair, and a fellowship from the European Research Council (ERC). Several of his works received substantial coverage in the national and international media.

Grégoire Courtine Associate Professor

Introduction

There are over 3,000 persons living with a spinal cord injury (SCI) in Switzerland, and several million worldwide. SCI leads to a range of disabilities that seriously diminish the patient’s quality of life. Over the past 15 years, we implemented an unconventional research program with the aim to develop radically new treatment paradigms to restore sensorimotor functions in severely paralyzed people. Our therapeutic interventions are developed in rodents and optimized in non-human primates, and clinical trials are in the implementation phase.

Keywords

Spinal cord injury, neural repair, neurorehabilitation, neuroprosthetics, brain-machine interface, robotic, neuronal recordings, optogenetic, EMG, kinematic, locomotion, neuromorphology, mice, rats, monkeys, humans.

Results Obtained in 2012

Over the past 10 years, we have developed, methodically, a series of neuroprosthetic technologies to enable motor control after neuromotor disorders. This includes an electrochemical spinal neuroprosthesis to transform lumbosacral circuits from non-functional to highly functional networks, and a robotic postural neuroprosthesis to establish optimal conditions of balance and support during rehabilitative training. In 2012, we introduced a treatment paradigm that combined all these neuroprosthetic technolo-

gies. We showed that rats with a spinal cord injury, leading to complete and permanent paralysis, regained supraspinal control over complex locomotor movements. Anatomical evaluations revealed that training encouraged the brain to elaborate a multiplicity of alternative pathways to regain access to the denervated spinal locomotor circuits. No previous interventions restored voluntary locomotor movements after a paralyzing SCI. Our objective is to translate these discoveries from rodents to a viable intervention for humans. To achieve this, we have gathered a highly multidisciplinary and synergistic team of advanced basic and clinical investigators at the EPFL and the CHUV. Through this network, we have developed an electrochemical spinal neuroprosthesis uniquely fitted to the human spinal cord, and robotic systems for rehabilitation of subjects with impaired gait. Upon validation by the ethical boards, these new technologies will be tested in spinal cord injured individuals. In parallel, we have established an advanced non-human primate model that will allow us to demonstrate the efficacy and safety of our interventions. Our aim is to prepare the second phase of clinical trials with refined neuroprosthetic technologies. We anticipate that 2013 will be a year full of new, exciting discoveries.

EPFL School of Life Sciences - 2012 Annual Report

Courtine G, Micera S, Digiovanna J, Del R Millán J. (2012) Brain-machine interface: closer to therapeutic reality? Lancet 2012 Dec 13. Van den Brand R, Heutschi J, barraud Q, Digiovanna J, Bartholdi K, Huerlimann M, Friedli L, Vollenweider I, Martin Moraud E, Duis S, Dominici N, Micera S, Musienko PE, Courtine G (2012) Restoring voluntary control of locomotion after paralyzing spinal cord injury. Science 336(6085): 1182-1185 Dominici N, Keller U, Vallery H, Friedli L, van den Brand R, Starkey ML, Musienko P, Riener R, Courtine G (2012) Novel robotic interface to evaluate, enable, and train locomotion and balance after neuromotor disorders. Nature Medicine 18(7):1142-7. Horst M, Heutschi J, den Brand RV, Andersson KE, Gobet R, Sulser T, Courtine G, Eberli D. (2012) Multisystem Neuroprosthetic Training Improves Bladder Function After Severe Spinal Cord Injury. J Urol. 2012 Oct 8. Musienko P, Courtine G, Tibbs JE, Kilimnik V, Savochin A, Garfinkel A, Roy RR, Edgerton VR, Gerasimenko Y (2012) Somatosensory control of balance during locomotion in decerebrated cat. Journal of neurophysiology 107:2072-2082. Musienko P, Heutschi J, Friedli L, den Brand R, Courtine G (2012) Multi-system neurorehabilitative strategies to restore motor functions following severe spinal cord injury. Experimental neurology 235:100-109. Nout YS, Ferguson AR, Strand SC, Moseanko R, Hawbecker S, Zdunowski S, Nielson JL, Roy RR, Zhong H, Rosenzweig ES, Brock JH, Courtine G, Edgerton VR, Tuszynski MH, Beattie MS, Bresnahan JC (2012) Methods for Functional Assessment After C7 Spinal Cord Hemisection in the Rhesus Monkey. Neurorehabilitation and neural repair 26(6):556-69. Nout YS, Rosenzweig ES, Brock JH, Strand SC, Moseanko R, Hawbecker S, Zdunowski S, Nielson JL, Roy RR, Courtine G, Ferguson AR, Edgerton VR, Beattie MS, Bresnahan JC, Tuszynski MH (2012) Animal models of neurologic disorders: a nonhuman primate model of spinal cord injury. Neurotherapeutics : 9:380-392. Courtine G, van den Brand R, Musienko P (2011) Spinal cord injury: time to move. Lancet 377:1896-1898. Musienko P, van den Brand R, Marzendorfer O, Roy RR, Gerasimenko Y, Edgerton VR, Courtine G (2011) Controlling specific locomotor behaviors through multidimensional monoaminergic modulation of spinal circuitries. J Neuroscience 31:9264-9278.

Team Members Postdoctoral Fellows Quentin Barraud David Borton Nadia Dominici Jean Laurens Cristina Martinez Gonzales Pavel Musienko Natalia Pavlova Rubia van den Brand Joachim von Zitzewitz PhD students Léonie Asboth Janine Beauparlant Lucia Friedli Wittler Isabel Vollenweider Fang Wang Nikolaus Wenger Marco Bonizzato Martin Moraud Eduardo Master’s Students Sélin Anil Steve Blachut Leonardo Caranzano Jérome Gandar Sam Ghazanfari Paul Giroud Nili Hamili Pierre-Yves Helleboid Hugo Hoedemaker Alexander Kuck Julie Kreider Bastien Martin Frédéric Michoud Audrey Nguyen JuneSeung Lee Solange Richter Livio Ruzzante Giorgio Ulrich Charles Vila Ambroise Vuaridel Numa Perez Technicians Kay Bartholdi Simone Duis Administrative Assistant Anne-Marie Rodel Stéphanie Bouchet

BMI - Brain Mind Institute

Selected Publications

A rat received a spinal cord injury leading to permanent paralysis. A robot-assisted training paradigm enabled by an electrochemical spinal neuroprosthesis restored supraspinal control over refined locomotion through the extensive and ubiquitous remodeling of neuronal pathways.

EPFL School of Life Sciences - 2012 Annual Report

Fraering Lab

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

Patrick Fraering

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 focused 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, synaptic activity and plasticity, therapeutic targets, translational research.

Results Obtained in 2012

Highly efficient production of γ-secretase and Fabs for use in structural studies. Although γ-secretase represents a prime target for structure-based design of therapeutic compounds to safely treat AD, the scarcity of its supply has been a major hurdle for determining its high-resolution structure. We applied a transposon-mediated multigene stable integration technology to produce active γ-secretase in mammalian cells in amounts adequate for crystallization studies and drug screening. The amounts of γ-secretase were sufficient for immunization of mice and generation of Fab fragments binding exposed regions of native γ-secretase, and therefore useful as specific tools to facilitate crystal formation. Our strategy is expected to contribute to the crystallization of γ-secretase and to be widely used for the production of other multiprotein complexes for applications in structural biology and drug development. Alzheimer’s disease-linked mutations in Presenilin-1 result in a drastic loss of activity in purified γ-secretase complexes. Mutations linked to familial AD are found most frequently in PSEN1, the gene encoding PS1, the

catalytic subunit of γ-secretase. 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 FAD-linked 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 to Aβ1-40 ratio, two mechanisms that are likely involved in the pathogenesis of AD. 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 human APPC99 adopting a native conformation, bound accessible Nor C-terminal epitopes of this substrate and led to reduced Aβ levels in vitro and in vivo. Label-free imaging of cerebral β-Amyloidosis with extended-focus optical coherence microscopy (xfOCM). We demonstrated label-free imaging of cerebral β-amyloidosis ex vivo and in a living mouse model of AD using xfOCM. This technique offers advantages in terms of high-resolution and deep imaging of Aβ deposits, in a minimally invasive way and without the administration of contrast agents, thereby precluding variations in data collection due to interindividual and intraindividual variability in the uptake of amyloid dyes/radioactive tracers. It may support translational applications to evaluate the efficacy of new Aβ-targeting therapeutic strategies.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

J.R.Alattia, M. Matasci, M. Dimitrov, L. Aeschbach, D.L. Hacker, F.M. Wurm, and P.C. Fraering. (2013). Highly efficient production of the Alzheimer’s γ-secretase integral membrane protease complex by a multi-gene stable integration approach. Biotechnol Bioeng. 2013 Jan 28. In press. I. Hussain, J. Fabrègue, S. Ousson, L. Anderes, F. Borlat, V. Eligert, S. Berger, M. Dimitrov, J.R. Alattia, P.C. Fraering, and D. Beher. (2013). Gamma Secretase Activating Protein, GSAP is not a major regulator of γ-secretase activity and amyloid-β generation. J Biol Chem. 2013 Jan 25;288(4):2521-31. T. Bolmont, A. Bouwens, C. Pache, M. Dimitrov, C. Berclaz, M. Villiger, B.M. Wegenast-Braun, T. Lasser, P.C. Fraering. (2012). Label-Free Imaging of Cerebral β-Amyloidosis with Extended-Focus Optical Coherence Microscopy. J Neurosci. 2012 Oct 17;32(42):14548-14556. J.R. Alattia, C. Schweizer, M. Cacquevel, M. Dimitrov, L. Aeschbach, M. OuladAbdelghani, P.C. Fraering. (2012). Generation of Monoclonal Antibody Fragments Binding the Native γ-Secretase Complex for Use in Structural Studies. Biochemistry. 2012 Nov 6;51(44):8779-90.

Team Members Postdoctoral Fellows Jean-René Alattia Eugenio Barone PhD students Jemila Houacine Mitko Dimitrov Sebastien Mosser Magda Palcynska Master’s Students Andrzej Fligier Alexandre Matz Technicians Lorene Aeschbach Justine Pascual Administrative Assistant Monica Navarro Suarez

M. Cacquevel, L. Aeschbach, J. Houacine, P.C. Fraering. (2012). Alzheimer’s disease-linked mutations in presenilin-1 result in a drastic loss of activity in purified γ-secretase complexes. PLoS One. 2012;7(4):e35133. Epub 2012 Apr 18. 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 Nov;33(11):2704-14. 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 J. 2011 Jul;25(7):2287-95.

BMI - Brain Mind Institute

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

In vivo longitudinal xfOCM imaging of cerebral Aβ amyloidosis (green) in a transgenic mouse model of Alzheimer’s disease.

EPFL School of Life Sciences - 2012 Annual Report

Gerstner Lab http://lcn1.epfl.ch/

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

Computational neuroscience, models of spiking neurons, models of synaptic plasticity and STDP, models of Learning.

Results Obtained in 2012

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. A review paper on these topics has appeared in Science. A scientific paper together with Carl Petersen was published in the Journal of Neurophysiology.

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 stabilization 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 has been published in 2012. A model of perceptual learning in vision has appeared in a paper with Michael Herzog.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

W. Gerstner, H. Sprekeler and G. Deco, (2012) Theory and Simulation in Neuroscience. Science, vol. 338, p. 60-65. R. Naud and W. Gerstner, (2012) Coding and Decoding with Adapting Neurons: A Population Approach to the Peri-Stimulus Time Histogram. Plos Computational Biology, vol. 8, num. 10, p. e1002711, 2012. M. Avermann, C. Tomm, C. Mateo, W. Gerstner and C. C. H. Petersen, (2012) Microcircuits of excitatory and inhibitory neurons in layer 2/3 of mouse barrel cortex. Journal of Neurophysiology, vol. 107, num. 11, p. 3116-3134. M. H. Herzog, K. C. Aberg, N. Frémaux, W. Gerstner and H. Sprekeler, (2012) Perceptual learning, roving and the unsupervised bias. Vision Research, vol. 61, p. 95-99. S. Mensi, R. Naud, C. Pozzorini, M. Avermann and C. C. H. Petersen et al. Parameter extraction and classification of three cortical neuron types reveals two distinct adaptation mechanisms, Journal Of Neurophysiology, vol. 107, num. 6, p. 1756-1775, 2012. 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.

Team Members Postdoctoral Fellows Moritz Deger Kerstin Preuschoff Tim Vogels

PhD students Dane Corneil Andrea De Antoni Mohammadjavad Faraji Nicolas Frémaux Felipe Gerhard Skander Mensi Christian Pozzorini Alex Seeholzer Hesam Setareh Carlos Stein Friedemann Zenke Lorric Ziegler Master’s Students Julien Duc Everton João Agnes William Podlaski Guillaume Riesen Varun Sharma Administrative Assistant Chantal Mellier

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

BMI - Brain Mind Institute

Inhibitory synaptic plasticity restores asynchronous irregular activity in recurrent network models. (A) Epileptic activity. (Top) heat map of the network firing where cells are arranged on a 2D grid. (Bottom) spike raster of different subpopulations of cells. (B) Activity after one hour of network activity in the presence of inhibitory synaptic plasticity. Network activity is stable and de-correlated at low activities. (C) Activity after two cell memories have been introduced in the excitatory weight matrix. (D) Activity after another hour. Memories have been masked by “anti memories”, but can be recalled by an external cue (E,F,G).

EPFL School of Life Sciences - 2012 Annual Report

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

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 has been 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 sense. Surprisingly, the neural and computational 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. In addition, we investigate vision in healthy aging and have established an endophenotype of schizophrenia based on visual masking.

Keywords

Spatio-temporal Vision (crowding, non-retinotopic processing, visual masking), Perceptual and Reinforcement Learning, Ageing & Schizophrenia Research.

Results Obtained in 2012

Crowding & Masking. In crowding, the perception of a target strongly deteriorates when flanked by neighboring elements. Crowding is usually explained by pooling models, which are well in the spirit of the hierarchical, feedforward model of object recognition. Neurons in higher visual areas, with larger receptive fields, pool information from lower level neurons. Because of pooling, features of the target and flanking elements are jumbled and so feature identification is lost. A prediction of these models is that crowding increases when adding flankers. We showed that to the contrary that adding flanks improves performance. (Manassi et al., 2012).

Perceptual learning & the power of the mind. Usually, it is believed that learning is driven by the repeated presentations of stimuli which change synaptic weights. No stimulus, no learning. We found that perceptual learning can occur even if there are no stimuli presented at all when observers imagine the stimuli- showing the power of the mind (Tartaglia et al. 2012; Mast et al., 2012). In collaboration with Wulfram Gerstner, we have identified a very general mathematical mechanism that explains why perceptual learning does not occur under roving conditions (Herzog et al., 2012). In collaboration with Carmen Sandi, we showed how stress influences perceptual learning (Aberg et al., 2012). In decision making, it is usually assumed that stimulus evidence drives a drift process towards one of two decision variables. We found that there is a silent evidence integration stage, which was overlooked previously. In collaboration with Wulfram Gerstner, we characterized these processes mathematically (Rüter et al., 2012).

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Rüter J, Marcille N, Sprekeler H, Gerstner W, Herzog MH (2012). Paradoxical Evidence Integration in Rapid Decision Processes. PLoS Computational Biology, 8(2), e1002382. Herzog MH, Aberg KC, Frémaux N, Gerstner W, Sprekeler H (2012). Perceptual learning, roving and the unsupervised bias. Vision Research, 61, p95-99. Plomp G, Kunchulia M, Herzog MH (2012). Age-related changes in visually evoked electrical brain activity. Human Brain Mapping, 33(5), p1124-1136. Manassi M, Sayim B, Herzog MH (2012). Grouping, pooling, and when bigger is better in visual crowding. Journal of Vision, 12(10), p1-14. Aberg K, Clarke A, Sandi C, Herzog MH (2012). Trait anxiety and post-learning stress do not affect perceptual learning. Neurobiology of Learning and Memory, 98(3), p246-53. Cappe C, Herzog MH, Herzig DA, Brand A, Mohr C (2012). Cognitive disorganisation in schizotypy is associated with deterioration in visual backward masking. Psychiatry Research, 200, p652-659. Plomp G, Michel CM, Herzog MH (2011). Electrical source dynamics in three functional localizer paradigms. Neuroimage, 54, p1763.

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

PhD Students Vitaly Chicherov Lukasz Grzeczkowski Mauro Manassi Izabela Szumska Evelina Thunell Master Student Sophie Lonchampt SHS Student Ophélie Favrod Engineer Marc Repnow Administrative Assistant Laure Dayer

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

BMI - Brain Mind Institute

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). In most conditions, it seems that elderly use very different brain areas to solve the visual tasks than younger controls. From: Plomp G, Kunchulia M, Herzog MH (2012) Age-related changes in visually evoked electrical brain activity. Hum Brain Mapp. 2012 May;33(5):1124-36. doi: 10.1002/hbm.21273. Epub 2011 Apr 29.

EPFL School of Life Sciences - 2012 Annual Report

Lashuel Lab

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

Hilal A. Lashuel received his B.Sc. degree in chemistry from the City University of New York in 1994 and his PhD in bioorganic 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

Research in the Lashuel laboratory focuses on applying chemical, biophysical, and molecular biology approaches to elucidate the molecular and structural basis of protein misfolding and aggregation and the mechanisms by which these processes contribute to the pathogenesis of neurodegenerative diseases. Current research efforts cover the following topics: (1) Elucidating the sequence, molecular and cellular determinants underlying protein aggregation, propagation and toxicity. (2) Developing innovative chemical approaches and novel tools to monitor and control protein folding, self-assembly and post-translation in vitro and in vivo with spatial and temporal resolution; and (3) developing novel therapeutic strategies to treat Parkinson’s disease based on modulating protein aggregation and clearance.

Keywords

Chemical Biology, protein folding, protein aggregation, post-translational modifications, protein synthesis amyloid, phosphorylation, neurodegeneration, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease.

Results Obtained in 2012

Chemical and semisynthetic strategies for Site-specific modification of proteins - Protein Post-translational modifications (PTMs) play important roles in regulating protein function and many biological processes and are increasingly implicated in the pathogenesis of several neurodegenerative diseases including Alzheimer’s, Parkinson’s and Huntington’s disease. Therefore a better understanding of how individual modifications and cross-talk between different modifications influence protein structure and function is essential to understanding the role of PTMs in health and disease. Our laboratory has developed and optimized for the first time multiple efficient synthetic and semisynthetic strategies that enable site-specific introduction of single or multiple PTMs into α-syn and exon1 of the Huntingtin protein (Httex1), two proteins that are linked to the pathogenesis of Parkinson’s and Huntington’s disease, respectively.

Using these semisynthetic proteins we were able to provide novel insight into the potential roles of diseases-associated α-syn on the native structure, aggregation, membrane binding, subcellular localization and protein-protein interactions of α-syn in vitro. Our results show that some of these modifications (phosphorylation at S87 and S129 and Uiquitination at K6) inhibit α-syn aggregation and protect against α-syn induced toxicity (pS87 and pS129). In addition, in collaboration with Dr. Ashraf Brik and Dr. Aaron Ciechanover group, we showed that mono-ubiquitination is sufficient to target α-syn for degradation by the proteasome, whereas phosphorylation at S129 by the Polo Like Kinase 2 (PLK2) targets α-syn for degradation by lysosomal-autophagic pathways. These findings highlight the potential role of PTMs in regulating α-syn degradation and suggest that the enzymes that regulate these modifications may constitute a viable therapeutic target for the treatment of PD and related synucleinopathies. Discovery of a novel aggregation and functional domain in the Huntingtin protein - Increasing evidence suggests that although the expanded polyQ in Htt and other proteins plays a central role in the pathogenesis of HD, it is not the sole determinant of Htt aggregation and toxicity. Through a systematic analysis of the N-terminal sequence of Htt, we discovered a novel amyloidogenic domain outside of exon1. A systematic analysis of peptides spanning different regions within this domain led to the identification of two distinct sequence motifs (106-116 and 128-135) that are responsible for the aggregation of this domain. Preliminary results using cellular models of Htt aggregation and toxicity suggest that the aggregation propensity of this novel amyloidogenic domain influence the rate and aggregation pathway of the NtHtt fragments and their toxicity. Further studies are currently underway in our laboratory to investigate potential cross-talk between the novel domains identified in this work and the polyQ repeat region and to elucidate their potential roles in regulating the physiological and pathogenic properties of the full-length protein and disease-associated N-terminal fragments in cell culture and animal models of HD.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Lashuel HA, Overk C, Ouelati A, and Masliah E (2012) “α-synuclein oliogmerizatoin in health and disease”, Nature Rev. Neuroscience. 14(1):38-48. Shabek N, Herman-Bachinsky Y, Buchsbaum S, Lewinson O, Haj-Yahya M, Hejjaoui M, Lashuel HA, Sommer T, Brik A, Ceichanover A. (2012) The size of the proteasomal substrate determines whether its degradation will be mediated by Mono- or Polyubiquitination. Mol. Cell. 12;48(1):87-97 Hejjaoui M, Butterfield S, Fauvet B, Vercryusse F, Cun J, Dikiy I, Prudent M, Olschewski D, Zhang Y, Eliezer D., Lashuel HA*. Chemical Biology of α-synuclein: Elucidating the role of C-terminal post-translational modifications using protein semisynthetic strategies: Phosphorylation at Tyrosine 125”, J. Amer. Chem. Soc. 21;134(11):5196-210. Oueslati A, Paleologou KE, Schneider BL, Aebischer P., Lashuel HA*. (2012) Mimicking phosphorylation at Serin87 inhibits the aggregation of human alphasynuclein and protects against its toxicity in a rat model of Parkinson’s disease, J. Neuroscience, 2012, 1;32(5):1536-44. Fauvet B., Mebfo MK, Fares BM, Desobry C, Michael S, Ardah MT, Tsika E, Coune P, Eliezer D, Moore DJ, Schneider B, Aebischer P., El-agnaf OM, Masliah E, and Lashuel HA*. (2012) Alpha-synuclein in the central nervous system, in mammalian cells, and produced by E. coli exists predominantly as a disorderd monomer. J. Biol. Chem, 287, 15345-15364

Team Members Postdoctoral Fellows Baillie Mark Burai Ritwik Mahul Mellier Anne-Laure Oueslati Abid Wang Zheming PhD Students Ansaloni Annalisa Ait Bouziad Nadine Desobry Carole Fares Mohamed-Bilal Fauvet Bruno Khalaf Ossama Mbefo Kamdem Martial Vercruysse Filip Master’s Student Chiki Anass Technical Staff Jordan Nathalie Perrin John Vocat Céline Administrative Assistants Favre Sandrine

Fauvet B, Fares BM, Samuel F, Kikiy I, Tandon A, Eliezer D, Lashuel HA*. (2012) Characterization of semisynthetic and natural N-terminal acetylated α-synuclein in vitro and in intact cells: Iimplications for α-synuclein aggregation and cellular properties” J. Biol. Chem. 17;287(34):28243-62. Butterfield S, Hejjaoui M, Fauvet B, and Lashuel HA*. (2012) Chemical approaches to elucidate the mechanisms of amyloid formation and toxicity. J. Mol. Biol. 421, 204-236 Hejjaoui H, Haj-Yahya M, Kumar KS, Brik A* and Lashuel HA. (2011) Towards elucidating the role of ubiquitination in the pathogenesis of Parkinson’s disease using semisynthetic ubquitinated α-synuclein”. Angew Chem Int Ed.10;50(2):405-9.

BMI - Brain Mind Institute

Schematic depictions illustrating the different semisynthetic and chemical strategies developed by our group to allow controlled and site-specific introduction of single or multiple modifications in different regions of α-synuclein.

EPFL School of Life Sciences - 2012 Annual Report

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

Pierre Magistretti is a professor at the Brain Mind Institute at EPFL and at the Center for Psychiatric Neuroscience of the University of Lausanne/CHUV and an 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. He was a recipient of the Theodore-Ott Prize (1997), was the international Chair (20072008) at the Collège de France, Paris, President of FENS (2002 – 2004) and IBRO Secretary General (2009-2012). Since October 2010, Dr. Magistretti is the director of NCCR SYNAPSY - “The synaptic bases of mental diseases”. Currently on sabbatical.

Pierre Magistretti

Full Professor Joint Chair EPFL/UNIL-CHUV

Introduction

two other related energy substrates, glucose and pyruvate, revealing a novel role of lactate as a signaling molecule. We will now extend the molecular characterization of this thus far unknown action of lactate. In particular we will explore the signaling mechanisms triggered by lactate on NMDA receptor activity.

Keywords

We have continued to explore the role of metabolic coupling between astrocytes and neurons in synaptic plasticity and in neuroprotection. In this context, we have promoted three very fruitful collaborations with groups that have provided us with access to well established in vivo models of learning and memory, neurodegeneration and stroke (Suzuki et al, 2011; Lee et al, 2012; Berthet et al, 2012). These studies have demonstrated in vivo a fundamental role of astrocyte-derived lactate, as predicted by the Astrocyte Neuron Lactate Shuttle (ANLS) model that we have proposed several years ago, in learning and memory and in neuroprotection (Pellerin and Magistretti, 2012).

We will continue the analysis of the plasticity in the expression of genes related to neuron-glia metabolic coupling during learning paradigms. Using (14C) 2-Deoxyglucose (2-DG) technique we have identified the brain areas that are engaged in context-dependent avoidance behavior in mice using the step-through inhibitory avoidance paradigm (IA). Regional brain metabolic activity, as measured by the 2DG uptake, was quantified in several brain regions. This metabolic mapping revealed increased glucose utilization in hippocampus, amygdala, anterior cingulate cortex and mammillary bodies. Microdissection of the dorsal hippocampus followed by qRT-PCR analysis has indicated that genes expressed by astrocytes such MCT 1, MCT 4, alpha2 subunit of the Na K-ATPase, Glut 1 and all genes coding for enzymes of glycogen metabolism are upregulated 3 and 24 hours after IA learning. We will now extend this analysis to longer time-points and to other brain areas that are engaged in the learning process as demonstrated by the 2-DG technique.

With Cristina Alberini’s group at NYU we have shown that astrocyte-derived lactate is necessary for the establishment of long term memory (LTM) as well as for the maintenance of long-term potentiation (LTP) in vivo in mice. Following up on these results we have demonstrated that lactate stimulates expression of genes related to synaptic plasticity such as Arc, Zif268 and BDNF in primary cultures of cortical neurons as well as in vivo. Biochemical and electrophysiological initial results show that this effect results from the modulation by lactate of ionotropic NMDA receptor activity. The effects of lactate on plasticity gene expression are blocked by the NMDA receptor antagonist MK 801. Furthermore the generation by lactate of a transient MK 801-sensitive inward current is necessary for gene expression induction. These effects are not observed with

We are continuing the application of Digital Holographic Microscopy (DHM) to the study of neuronal and glial dynamics. Thus we have been able to monitor the transmembrane water fluxes resulting from the activation of glutamate ionotropic receptors and of the co-transporters KCC2 and NKCC1 (Jourdain et al, 2011). In addition, this optical monitoring of transmembrane water movements has also been efficiently used to simultaneously record in multiple cells chloride current associated to activation of the ligand-gated chloride channel GABAA receptor (Jourdain et al, in press). The quantitative phase signal monitored with DHM followed by appropriate numerical analysis has allowed us to detect optical signs of early cell death (Pavillon et al, 2012) with which we can test the potential neurprotective effects of a variety of compounds, including lactate (see above).

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

Results Obtained in 2012

EPFL School of Life Sciences - 2012 Annual Report

Team Members

Selected Publications

Jourdain P., Boss D., Rappaz B., Moratal C., Hernandez M.C., Depeursinge C., Magistretti P.J. and Marquet P. (2012). Simultaneous optical recording in multiple cells by digital holographic microscopy of chloride current associated to activation of the ligand-gated chloride channel GABA(A) receptor. PLoS One. 7(12):e51041. Berthet C., Castillo X., Magistretti P.J. and Hirt L. (2012). New evidence of neuroprotection by lactate after transient focal cerebral ischaemia: extended benefit after intracerebroventricular injection and efficacy of intravenous administration. Cerebrovasc Dis. 34(5-6):329-35.

Senior Scientist Gabriele Grenningloh Scientists Igor Allaman Nicolas Aznavour Stéphane Chamot Pascal Jourdain Sylvain Lengacher Jean-Marie Petit Jiangyan Yang

Lee Y., Morrison B.M., Li Y, Lengacher S., Farah M.H., Hoffman P.N., Liu Y., Tsingalia A., Jin L., Zhang P.W., Pellerin L., Magistretti P.J. and Rothstein J.D. (2012). Oligodendroglia metabolically support axons and contribute to neurodegeneration. Nature. 487(7408):443-8.

PhD Students Daniel Boss Benjamin Boury-Jamot Elena Migacheva Monika Saxena Manuel Zenger

Pavillon N., Kühn J. Moratal C., Jourdain P., Depeursinge C., Magistretti P.J. and Marquet P. (2012). Early cell death detection with digital holographic microscopy. PLoS One. 7(1):e30912.

Master’s Students Johannes Kacerovsky Anna Mikhaleva

Bélanger M., Yang J., Petit J.M., Laroche T., Magistretti P.J.* and Allaman I.* (2011). Role of the glyoxalase system in astrocyte-mediated neuroprotection. J Neurosci. 31(50):18338-52. * Co-last authors.

Technicians Cendrine Barrière Elena Gasparotto Joel Gyger Evelyne Ruchti

Jourdain P., Pavillon N., Moratal C., Boss D., Rappaz B., Depeursinge C., Marquet P. and Magistretti P.J. (2011). Determination of Transmembrane Water Fluxes in Neurons Elicited by Glutamate Ionotropic Receptors and by the Cotransporters KCC2 and NKCC1: A Digital Holographic Microscopy Study. J Neurosci. 31(33):11846-54. Lavoie S., Allaman I., Petit J.M., Do K.Q. and Magistretti P.J. (2011). Altered glycogen metabolism in cultured astrocytes from mice with chronic glutathione deficit; relevance for neuroenergetics in schizophrenia. PLoS One. 6(7):e22875.

Trainee Biology Laboratory Assistant Nathalie Bigler Administrative Assistant Monica Navarro Suarez

Wyss M.T., Jolivet R., Buck A., Magistretti P.J. and Weber B. (2011). In vivo evidence for lactate as a neuronal energy source. J Neurosci. 31(20):7477-85.

BMI - Brain Mind Institute

Suzuki A., Stern S.A., Bozdagi O., Huntley G.W., Walker R.H., Magistretti P.J.* and Alberini C.M.* (2011). Astrocyte-neuron lactate transport is required for long-term memory formation. Cell. 144(5):810-23 *Corresponding authors.

High expression of Glo-1 in astrocytes of the mouse cerebral cortex, This enzyme is important for the detoxification of methylglyoxal, a cytotoxic by product of glycolysis. 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.

EPFL School of Life Sciences - 2012 Annual Report

Markram Lab http://bmi.epfl.ch/

Henry Markram Full Professor

Henry Markram is the Principal Investigator of the Laboratory of Neural and Microcircuitry, the Director of the Blue Brain Project, and the Co-Director of the recently awarded FET flagship, the Human Brain Project. (p. 14) He began his research career in South Africa in the early 1980s, later moving to Israel and then to the EPFL, where he founded the Brain Mind Institute in 2002. Since the start of his career, he has focused on neural microcircuitry, applying a broad range of anatomical, physiological, biophysical and molecular techniques, and pioneering the multi-neuron patch-clamp approach. His best-known discoveries are the principles of Spike Timing Dependent Plasticity (STDP), Redistribution of Synaptic Efficacy (RSE), and Long-Term Microcircuit Plasticity (LTMP). He has worked with theoreticians to develop the concept of “liquid computing”, a novel technique for handling real time continuous input to recurrent neural networks. He has also been active in autism research, a field in which he has co-developed the Intense World Theory of Autism.

Introduction

The Laboratory of Neural Microcircuitry (LNMC) is dedicated to understanding the structure, function and plasticity of the microcircuitry of the neocortex. To investigate these neocortical microcircuits, LNMC makes use of state of art technologies including: multi-neuron patch-clamp technologies, automated patch clamp, multi-electrode arrays (MEAs), photo-activation, a variety of imaging systems including fast CCD imaging, 2 photon and ultramicroscopy, 3D reconstruction, high throughput, single neuron gene expression profiling (mRNA-seq) and multiplex RT-PCR, microfluidics, informatics tools, and supercomputers.

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 2012

The Research in the lab is organized into a number of projects, namely: Transcriptomics of neuron populations and single cells The aim of this research project is to correlate the electrical and structural properties of individual neurons with the genes they express. Expression profiles have been obtained from as little as 100 FACS sorted cells, serving as proof of principle for the novel method developed in LNMC to extract and sort fluoresenctly tagged cells from tissue. Channelome - The aim of the Channelome project is to characterize biophysics of these ion channels in a controlled and consistent environment with an automated patch clamp setup. Currently, we have more than 50 stable cell lines expressing individual ion channels, which are ready for analysis. Channelpedia has been developed to systematically store all the data generated by the Channelome project.

Neuroanatomy - Using 3D reconstructions of neurons in slices combined with immunohistochemistry and whole mount imaging of brains, our goal is to map: 1) the complete set of cortical neuron morphologies, 2) the relative composition of cortical neuron subtypes, and 3) the long range projections between cortical microcircuits and other brain structures. We currently have close to 1000 reconstructed neuron morphologies from the somatosensory cortex, and we are expanding this to other cortical areas as well. Electrophysiology & Microcircuits - We use up to 12 multi-patch clamp setups to study the individual neuronal properties and quantify the principles of local connectivity between these neurons (microcircuits). Plasticity - LNMC studies short and long-term plasticity, occurring under different time scales ranging from few milliseconds to hours. We are currently focusing on the role of STDP in the context of network activity using MEA stimulation in combination with patch clamp recordings. Neuromodulation - To start mapping the intricate relationship between the cortex and subcortical nuclei containing the neuromodulatory neurons, LNMC has engaged in a consortium (DDPDGENES) that aims to characterize the properties of dopaminergic (DA) cells across development and aging in both mouse and human tissue. Autism - The aim of our group is to address if neural microcircuitry hyper-functioning is at the heart of the neuropathology of autism, as predicted by the Intense World Theory. In our current investigations we try to address if autism is characterized by disproportionately stronger emotional responses to stimulation, due to limbic hyper-functionality.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Postdoctoral Fellows/ Research Staff Christodoulou Dimitri Marco Hagens Olivier Logette Emmanuelle Markram Kamila Perin Rodrigo de Campos Petitprez Séverine Pezzoli Maurizio Ferdinando Rajnish Ranjan Ryge Jesper Svensson Erik Anders PhD Students Delattre Vincent Favre Mônica Ghobril Jean Pierre Muralidhar Shruti

Khazen G, Hill SL, Schürmann F, Markram H (2012) Combinatorial Expression Rules of Ion Channel Genes in Juvenile Rat (Rattus norvegicus) Neocortical Neurons. PLoS ONE 7(4): e34786. doi:10.1371/journal.pone.0034786.

Trainees Achouri Karim Perrenoud Matthieu Ludovic Rakonjac Marija

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.

Technical Staff Herzog Mirjia La Mendola Deborah Meystre Julie

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

External Employee Giugliano Michele Administrative Assistant Christiane Debono

F.Tauheed, T.Heinis, F.Schürmann, H.Markram, A.Ailamaki: SCOUT: Prefetching of Latent Structure Following Queries, VLDB 2012 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

BMI - Brain Mind Institute

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

Neurons in brain slices are patched via multi neuron patch-clamp setups and then stained with biocytin before they can be computationally reconstructed in 3D.

EPFL School of Life Sciences - 2012 Annual Report

Moore Lab

http://moorelab.epfl.ch/

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, Baltimore. 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

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 pathophysiology 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 neurodegeneration. We aim to use this information in to develop novel strategies to delay or prevent this devastating disease.

Keywords

Parkinson’s disease, parkinsonism, neurodegeneration, genetic mutations, disease models, neuronal cell death, leucine-rich repeat kinase 2 (LRRK2), α-synuclein, ATP13A2, VPS35, therapeutic targets.

Results Obtained in 2012

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), α-synuclein, ATP13A2 and VPS35. Mutations in the LRRK2, α-synuclein and VPS35 genes cause autosomal dominant forms of PD, whereas ATP13A2 mutations cause autosomal recessive PD. Mutations in the LRRK2 gene were first discovered in 2004 and we have focused over the years to understand and model the pathogenic effects of these dominant mutations in simple model organisms such as the baker’s yeast, Saccharomyces cerevisiae, cultured neurons, and rodent models. In 2012, we extended our observations from a simple yeast model of LRRK2-dependent cytotoxicity where we previously identified a number of novel genetic modifiers of toxicity. We recently demonstrated that the mammalian ortholog of one of these yeast genes, ADP-ribosylation factor GTPase-activating protein 1 (ArfGAP1), acts as a novel regulator of LRRK2 enzymatic activity and neuronal toxicity, and also serves as a kinase substrate of LRRK2. Importantly, inhibition of ArfGAP1 provided neuroprotection

against LRRK2 in cultured neurons and we are currently validating these effects in animal models of PD and dissecting the underlying mechanism involved. In other work, we have explored the relationship between the two dominant PD gene products, LRRK2 and α-synuclein, in animal models. We have been able to demonstrate that PD-related neurodegenerative phenotypes that develop in α-synuclein transgenic mice occur independent of LRRK2 expression suggesting that LRRK2 does not mediate α-synucleindependent neuronal damage in vivo. We are currently evaluating whether α-synuclein expression is oppositely required for LRRK2-dependent neurodegeneration in animal models in order to define common pathological pathways leading to PD. In 2012, we have also continued to develop a novel adenoviral-mediated gene transfer model for delivering disease-associated human LRRK2 variants to the nigrostriatal dopaminergic pathway of rodents, the neuronal circuit that selectively degenerates in PD. This new rodent model of LRRK2-associated PD will prove essential for understanding the molecular basis of familial LRRK2 mutations in precipitating neurodegeneration. Finally, our research is attempting to clarify the mechanisms underlying neuronal cell death induced by mutated LRRK2 and here we continue to explore the role of novel proteins or protein complexes that functionally interact with or are phosphorylated by LRRK2. In 2012 we continued to investigate the function and pathological dysfunction of the ATP13A2 protein. ATP13A2 is a novel P5-type ATPase protein that is thought to actively transport an unknown substrate across lysosomal membranes. We are attempting to understand the normal function of ATP13A2 in neurons and the pathogenic effects of familial mutations. Furthermore, we are creating rodent models based upon viral-mediated gene silencing to understand the effects of recessive “loss-of-function” mutations. We have also continued with a relatively new project to understand the contribution of VPS35 to PD. Our work is exploring the pathogenic effects of VPS35 mutations in yeast, neuronal and rodent models.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Team Members

Podhajska, A., Musso, A., Trancikova, A., Stafa, K., Moser, R., Glauser, L., Sonnay, S., Moore, D.J. (2012). Common pathogenic effects of missense mutations in the P-type ATPase ATP13A2 (PARK9) associated with early-onset parkinsonism. PLoS One 7(6): e39942.

PhD Students Alice Biosa Alessandra Musso Agata Podhajska Klodjan Stafa

Biosa, A., Trancikova, A., Civiero, L., Glauser, L., Bubacco, L., Greggio, E., Moore, D.J. (2013). GTPase activity regulates kinase activity and cellular phenotypes of Parkinson’s disease-associated LRRK2. Hum. Mol. Genet. 22(6): 1140-56.

Daher, J.P.L., Pletnikova, O., Biskup, S., Musso, A., Gellhaar, S., Galter, D., Troncoso, J.C., Lee, M.K., Dawson, T.M., Dawson, V.L., Moore, D.J. (2012). Neurodegenerative phenotypes in an A53T α-synuclein transgenic mouse model are independent of LRRK2. Hum. Mol. Genet. 21(11): 2420-31. Stafa, K., Trancikova, A., Webber, P.J., Glauser, L., West, A.B., Moore, D.J. (2012). GTPase activity and neuronal toxicity of Parkinson’s disease-associated LRRK2 is regulated by ArfGAP1. PLoS Genet. 8(2): e1002526. Ramonet, D., Podhajska, A., Stafa, K., Sonnay, S., Trancikova, A., Tsika, E., Pletnikova, O., Troncoso, J.C., Glauser, L., Moore, D.J. (2012). PARK9-associated ATP13A2 localizes to intracellular acidic vesicles and regulates cation homeostasis and neuronal integrity. Hum. Mol. Genet. 21(8): 1725-43.

Postdoctoral Fellows Guillaume Daniel Roger Moser Alzbeta Trancikova Elpida Tsika

Master’s Students Duygu Bas Aris Fiser Caroline Foo Meghna Kannan Laboratory technician Liliane Glauser Administrative Assistant Caroline Rheiner

Ramonet, D., Daher, J.P.L., Lin, B.M., Stafa, K., Kim, J., Banerjee, R., Westerlund, M., Pletnikova, O., Glauser, L., Yang, L., Liu, Y., Swing, D.A., Beal, M.F., Troncoso, J.C., McCaffery, J.M., Jenkins, N.A., Copeland, N.G., Galter, D., Thomas, B., Lee, M.K., Dawson, T.M., Dawson, V.L., Moore, D.J. (2011). Dopaminergic neuronal loss, reduced neurite complexity and autophagic abnormalities in transgenic mice expressing G2019S mutant LRRK2. PLoS One 6(4): e18568. Dusonchet, J., Kochubey, O., Stafa, K., Young, S.M., Zufferey, R., Moore, D.J., Schneider, B.L., Aebischer, P. (2011). A rat model of progressive nigral neurodegeneration induced by the Parkinson’s disease-associated G2019S mutation in LRRK2. J. Neurosci. 31(3): 907-12.

BMI - Brain Mind Institute

Xiong, Y., Coombes, C.E., Kilaru, A., Li, X., Gitler, A.D., Bowers, W.J., Dawson, V.L., Dawson, T.M., Moore, D.J. (2010). GTPase activity plays a key role in the pathobiology of LRRK2. PLoS Genet. 6(4): e1000902.

Models of familial Parkinson’s disease: LRRK2. (A) 2D phospho-proteome profiling of brain tissue from LRRK2 transgenic mice. (B) Degeneration of dopaminergic neurons in the substantia nigra of LRRK2 transgenic mice. (C) Accumulation of autophagosomes in the brain of G2019S LRRK2 mice. (D) Adenoviral (rAd)-mediated expression of human LRRK2 in midbrain dopaminergic (TH) neurons. Lower panel: protein architecture and familial mutations of LRRK2.

EPFL School of Life Sciences - 2012 Annual Report

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

Carl Petersen studied physics as a bachelor student in Oxford (1989-1992). During his PhD studies under the supervision of Prof. Michael Berridge in Cambridge (1992-1996), he investigated cellular and molecular mechanisms of calcium signalling. In his first postdoctoral period (1996-1998), he joined the laboratory of Prof. Roger Nicoll to investigate synaptic transmission and plasticity in the hippocampus. During a second postdoctoral period with Prof. Bert Sakmann (1999-2003), he began working on the primary somatosensory barrel cortex, investigating cortical circuits and sensory processing.

Carl Petersen

Associate Professor

Introduction

Carl Petersen joined the Brain Mind Institute of the Faculty of Life Science at the Ecole Polytechnique Federale de Lausanne (EPFL) in 2003, setting up the Laboratory of Sensory Processing to investigate the functional operation of neural circuits in mice during quantified behavior. The goal is 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. Our experiments focus primarily on tactile sensory perception in the mouse whisker sensorimotor system.

Keywords

Sensory perception; motor control; sensorimotor integration; learning; neocortex; neural circuits; synaptic transmission; whole-cell membrane potential recording; optogenetics; two-photon microscopy.

Results Obtained in 2012

Research in the Laboratory of Sensory Processing during 2012 contributed to three important areas of neuroscience in which we advanced towards our goal of a causal and mechanistic description of neural circuit function in sensory perception: Synaptic Connectivity of Neocortical Microcircuits (Avermann et al., 2012) Synaptic interactions between nearby excitatory and inhibitory neurons in the neocortex are thought to play fundamental roles in sensory processing. Here, we combine optogenetic stimulation and multiple simultaneous wholecell recordings in vitro to define key functional microcircuits within layer 2/3 of mouse primary somatosensory barrel cortex. A simple computational model based on the experimentally determined electrophysiological properties of the different classes of layer 2/3 neurons and their unitary synaptic connectivity accounted for key aspects of the network activity evoked by optogenetic stimulation, including the strong recruitment of fast-spiking GABAergic

neurons acting to suppress firing of excitatory neurons. We conclude that fast-spiking GABAergic neurons play an important role in neocortical microcircuit function through their strong local synaptic connectivity, which might contribute to driving sparse coding in excitatory layer 2/3 neurons of mouse barrel cortex in vivo. Cell-type Specific Function of Neocortical Microcircuits (Gentet et al., 2012) Neocortical GABAergic neurons have diverse molecular, structural and electrophysiological features, but the functional correlates of this diversity are largely unknown. Here, in this study, we reported unique membrane potential dynamics of somatostatin-expressing neurons in layer 2/3 of the primary somatosensory barrel cortex of awake behaving mice. Somatostatin-expressing neurons were spontaneously active during periods of quiet wakefulness. However, somatostatin-expressing cells hyperpolarized and reduced action potential firing in response to both passive and active whisker sensing, in contrast to all other recorded types of nearby neurons, which were excited by sensory input. Optogenetic inhibition of somatostatin-expressing neurons increased burst-firing in nearby excitatory neurons. We hypothesize that the spontaneous activity of somatostatin-expressing neurons during quiet wakefulness provides a tonic inhibition to the distal dendrites of excitatory pyramidal neurons. Conversely, the inhibition of somatostatin-expressing cells during active cortical processing likely enhances distal dendritic excitability, which may be of critical importance for top-down computations and sensorimotor integration. Thalamic control of cortical states (Poulet et al., 2012) In thus study, we investigated the impact of thalamus on ongoing cortical activity in the awake, behaving mouse. We demonstrated that the desynchronised cortical state during active behavior is driven by a centrally generated increase in thalamic action potential firing, which can also be mimicked by optogenetic stimulation of the thalamus. The thalamus therefore plays a key role in controlling cortical states.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Avermann, M., Tomm, C., Mateo, C., Gerstner, W. and Petersen, C.C.H. (2012). Microcircuits of excitatory and inhibitory neurons in layer 2/3 of mouse barrel cortex. J. Neurophysiol. 107: 3116-3134. Gentet, L.J., Kremer, Y., Taniguchi, H., Huang, Z.J., Staiger, J.F., Petersen, C.C.H. (2012). Unique functional properties of somatostatin-expressing GABAergic neurons in mouse barrel cortex. Nat. Neurosci. 15: 607-612. Mensi, S., Naud, R., Pozzorini, C., Avermann, M., Petersen, C.C.H. and Gerstner, W. (2012). Parameter extraction and classification of three cortical neuron types reveals two distinct adaptation mechanisms. J. Neurophysiol. 107: 17561775.

Team Members Postdoctoral Fellows Sylvain Crochet Emmanuel Eggermann Taro Kiritani Natalya Korogod Yves Kremer Alexandros Kyriakatos Damien Lapray Szabolcs Olah Shankar Sachidhanandam Tanya Sippy Nadia Urbain Takayuki Yamashita

Poulet, J.F.A., Fernandez, L.M., Crochet, S. and Petersen, C.C.H. (2012). Thalamic control of cortical states. Nat. Neurosci. 15: 370-372.

PhD Students Aurelie Pala Varun Sreenivasan

Mateo, C., Avermann, M., Gentet, L.J., Zhang, F., Deisseroth, K. and Petersen, C.C.H. (2011). In vivo optogenetic stimulation of neocortical excitatory neurons drives brain-state-dependent inhibition. Curr. Biol. 21: 1593-1602.

Administrative Assistant SĂŠverine Janot

Crochet, S., Poulet, J.F.A., Kremer, Y. and Petersen, C.C.H. (2011). Synaptic mechanisms underlying sparse coding of active touch. Neuron 69: 1160-1175.

BMI - Brain Mind Institute

Whole-cell recording electrodes (red fluorescence) were targeted using a two-photon microscope to two excitatory pyramidal neurons (Cell 1 and Cell 2) and one GFP-labelled (green) fast-spiking inhibitory GABAergic neuron (Cell 3) in a brain slice from a GAD67-GFP mouse (Avermann et al., 2012).

EPFL School of Life Sciences - 2012 Annual Report

Sandi Lab

http://lgc.epfl.ch/

Carmen Sandi was trained in Psychology and carried out her Ph.D. studies in Behavioral Neuroscience at the Cajal Institute, Madrid, in Spain. After postdoctoral appointments at the University of Bordeaux and the Open University, UK, she was recruited by UNED in Madrid, where she headed the Stress and Memory Lab. After a sabbatical year in the University of Bern, she joined the EPFL in 2003. Her goal is to understand how stress affects brain function and behavior. She has presided the European Brain and Behavior Society and is Editor-inChief of the journal Frontiers in Behavioral Neuroscience.

Carmen Sandi Full Professor Director of BMI

Introduction

The Laboratory of Behavioral Genetics investigates the impact and mechanisms whereby stress affects brain function and behavior, with a focus on the social domain. We are particularly interested in understanding the link between stress, personality traits and pathological aggression and social hierarchies both, under normal conditions and in the framework of psychopathology. Our work has highlighted glucocorticoid pathways as critical mediators of stress effects. Our goal is to uncover key neurobiological mechanisms and to develop opportunities for intervention on stress-related disorders.

Keywords

Stress, glucocorticoids, aggression, social hierarchy, psychopathology, anxiety, personality, neural cell adhesion molecules, mitochondrial function, psychopharmacology, optogenetics, neuroeconomics.

Results Obtained in 2012

Exposure to adverse experiences during childhood and adolescence has been associated with the development of psychiatric disorders, including increased aggression. We have developed an animal model based on exposure of outbred rats to fearful experiences during the peripuberty period that recapitulates the key features of a â&#x20AC;&#x2DC;cycle of violenceâ&#x20AC;&#x2122;: peripuberty stressed males become abnormally aggressive against both other males and females. The females that cohabitate with them develop behavioral, endocrine and neurobiological alterations. Their male offspring (despite not having been in contact with their fathers or exposed themselves to any experimental stress) show, as well, increased aggressive behaviors. Peripuberty stress induces as well other important behavioral alterations. This animal model allows us to investigate the effector pathways from stress to pathological aggression. We have found that peripuberty stressed rats exhibit alterations in the activation of the amygdala and the medial orbitofrontal cortex, as well as in their connectivity patterns. We have identified changes in the expression and epigenetic control

of genes from the serotonergic pathway in the prefrontal cortex, and verified that their pharmacological blockade (i.e., administration of a MAOA inhibitor) reversed the peripuberty stress-induced antisocial behaviors. As potential molecular mechanisms linking stress and asocial and aggressive behaviors, we have recently investigated on the role of synapse-specific cell adhesion molecules (this work relates to the FP7 EU project MemStick that we have coordinated). We have focused on the involvement of molecules of the nectin and neuroligin families in the social and cognitive abnormalities induced by stress. While information regarding nectins involvement in brain function and behavior is scarce, the neurexin-neuroligin transsynaptic adhesion complexes (neuroligin-1 associated with excitatory, while neuroligin-2 with inhibitory synapses) have revealed highly important for cognitive function, particularly social behaviors. Stress leads to profound structural and molecular changes in several brain regions, notably including the hippocampus. We have identified specific alterations in neuroligin-2 and nectin-3 in the hippocampus of rats submitted to stress protocols that result in alterations in cognitive and social (reduced social exploration and increased aggression). Importantly, we found evidence that the specific reduction of nectin-3 in the perisynaptic CA1 compartment after chronic stress is causally linked with stress-induced deficits in a CA1-dependent cognitive task and in social behaviors in experiments involving AAV-induced overexpression of nectin-3. We also found increased gelatinase activity in chronically stressed animals, which along with cell culture and pharmacological experiments implicated a role for matrix metalloproteinase (MMP) activity in the cleavage of nectin-3 in an NMDA-receptor-dependent mechanism. Our results are pioneer in indicating that stress impairs social behaviors by regulating mechanisms implicated in neurodevelopmental disorders that course with alterations in the social domain (e.g., autism, schizophrenia).

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Cordero, M.I., Poirier, G.L., Marquez, C., Veenit, V., Fontana, X., Salehi, B., Ansermet, F. and Sandi, C. (2012) Evidence for biological roots in the transgenerational transmission of intimate partner violence. Transl. Psychiatry 2:e106. Knafo, S., Venero, C., Sanchez-Puelles, C., Pereda-Perez, I., Franco, A., Sandi, C., et al. DeFelipe, J. and Esteban, J.A. (2012) Facilitation of AMPA receptor synaptic delivery as a molecular mechanism for cognitive enhancement. PLoS Biol. 10:e1001262. Castro, J.E., Diessler, S., Varea, E., Márquez, C. and Larsen, M.H., Cordero, M.I. and Sandi, C. (2012) Personality traits in rats predict vulnerability and resilience to developing stress-induced depression-like behaviors, HPA axis hyperreactivity and brain changes in pERK1/2 activity. Psychoneuroendocrinology 37:1209-1223. 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. Mol. Psychiatry 16:533-547. 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 36:2349-2356. Sandi C. (2011) Glucocorticoids act on glutamatergic pathways to affect memory processes. Trends Neurosci. 34:165-176. 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(1):56-71. Sandi C. (2011) Healing anxiety disorders with glucocorticoids. Proc. Natl. Acad. Sci. USA 108:6343-6344.

Team Members

Postdoctoral Fellows Alexandre Claude Gustave Bacq Samuel Bendahan Martina Fantin Fiona Hollis Guillaume Poirier Ricardo Ramires Orbicia Riccio Wicht John Christian Thoresen Michael van der Kooij External Employee Maria Isabel Cordero Campana PhD Students Laura Lozano Montes Stamatina Tzanoulinou Vandana Veenit Sophie Elisabeth Walker Scientific Assistant Christine Kohl Lab Technicians Céline Fournier Jocelyn Grosse Olivia Zanoletti Trainees Shishir Balyian Eleni Batzianouli Lejla Colic Matthijs de Boer Clara Garcia Mompo Leyla Loued-Khenissi Aurélie Papilloud Julia Simon Alina Strasser Agnieszka Szpakowska Ipshita Zutshi Students Damien Huzard Aya Imam Natsuko Imamura Alain Jacot-Guillarmod Doris Li Martin Vogel Academic Guest Lorenz Goette

BMI - Brain Mind Institute

Administrative Assistant Barbara Goumaz

Early life experiences are critical for determining neurodevelopmental trajectories linked to mental health or psychopathology. In the image, a pubertal rat is exposed to a harmless novel environment.

EPFL School of Life Sciences - 2012 Annual Report

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

Ralf Schneggenburger obtained a PhD in Natural Sciences at the University of Göttingen in 1993, and was a post-doctoral fellow at the University of Saarland (1994) and at the Ecole Normale Supérieure (1994 - 1996). During further postdoctoral work 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 at EPFL and has since then been leading the Laboratory for Synaptic Mechanisms at the Brain Mind Institute.

Ralf Schneggenburger Full Professor

Introduction

The main interest of the lab lies in understanding the cellular and molecular mechanisms of neuronal communication at synapses. We investigate basic mechanisms of transmitter release and its short- and long-term plasticity, and we also study activity dependent and -independent signaling mechanisms which determine synapse connectivity and synapse function at specific points in neuronal circuits. This research aims to gain insight into neuronal network function, and it forms the basis for understanding the pathophysiology of neuropsychiatric and neurodegenerative disorders, many of which represent diseases of the synapse.

Keywords

Synaptic transmission, nerve terminal, neurotransmitter, exocytosis, short-term plasticity, synapse development, synapse specificity, synapse connectivity, axonal signaling.

Results Obtained in 2012

We use an exceptionally large synapse located in the auditory pathway, the calyx of Held, at which we can gain access to the physiology of the presynaptic nerve terminal (see Figure 1). In 2012, we could show a relation between axon midline crossing, and the later functional maturation of the calyx of Held synapse (Michalski et al. 2013). At the calyx of Held projection, synapses usually strictly form on the opposite, “contralateral” brain side. In conditional Robo3 KO mice which lack Robo3 specifically in the lower auditory system, essentially all calyces of Held formed on the wrong, ipsilateral side of the brain. Ipsilateral calyces of Held were nearly normal in morphological terms, except for a slight deficit in the elimination of competing synaptic inputs. The functional maturation of ipsilateral calyces of Held was, however, strongly impaired. Thus, the excitatory postsynaptic currents (EPSCs) were smaller and had irregularities in their rising phase, indicating fewer released vesicles and more asynchronous release. Presyn-

aptic plasticity like post-tetanic potentiation (PTP), which normally disappears during development due to more effective Ca2+ ion handling in the nerve terminal, persisted with development in the Robo3 cKO mice. Some of the functional changes in synaptic transmission persisted up to adulthood in Robo3 cKO mice. These data indicate an apparent coupling between the development of synapse function, and the location of an output synapse in terms of the “correct” side of the brain. This coupling might serve to limit the influence of mis-localized synapses on the computations performed in a neuronal circuit. Further work needs to decipher the molecular mechanisms leading to the apparent coupling between functional synapse development and axon localization; perturbed axonal protein translation and related signaling deficiencies in Robo3 cKO mice might be involved. In a collaborative study with the laboratory of Prof. P. Aebischer (Gaugler et al., 2012), we elucidated the role of the presynaptic protein α-Synuclein in the pathogenesis of Parkinson’s Disease (PD). Some familial forms of PD are associated with multiplications of the α-Synuclein gene locus. To model the disease initiation in the dopaminergic nigrostriatal projection which is most relevant for PD, we moderately overexpressed the protein in the substantia nigra of rats, using adeno-associated viral vectors (AAV). Rats with unilateral overexpression of α-Synuclein in the substantia nigra showed significant asymmetries in spontaneous and drug-induced rotational motor behaviors as a sign of hemiparkinsonian impairments. The behavioral changes were associated with functional deficits in striatal dopamine release and ultrastructural changes in dopaminergic fibers, like a decreased density of dopaminergic vesicles and contact sites. Importantly, these axonal and presynaptic changes exceeded dopaminergic neuron- or fiber loss, indicating that an impaired function at dopaminergic synapses is an early component in this form of PD.

EPFL School of Life Sciences - 2012 Annual Report

Selected Publications

Michalski, N., Babai, N., Renier, N., Perkel, D.J., Chedotal, A., and Schneggenburger, R. (2013). Robo3-driven axon midline crossing conditions functional maturation of a large commissural synapse. Neuron 78, in press. Schneggenburger, R., Han, Y., Kochubey, O. (2012). Ca2+ channels and transmitter release at the active zone. Cell Calcium 52: 199 - 207. Gaugler M.N., Genç O., Bobela W., Mohanna S., Ardah M.T., El-Agnaf O.M., Cantoni M., Bensadoun J.C., Schneggenburger R., Knott G.W., Aebischer P., Schneider B.L. (2012) Nigrostriatal overabundance of α-synuclein leads to decreased vesicle density and deficits in dopamine release that correlate with reduced motor activity. Acta Neuropathologica, 123:653-69. Kochubey, O., Lou, X., and Schneggenburger, R. (2011). Regulation of transmitter release by Ca2+ and synaptotagmin: insights from a large CNS synapse. Trends in Neurosciences 34: 237-246. Han, Y., Kaeser, P. S., Südhof, T. C., and Schneggenburger, R. (2011). RIM determines Ca2+ channel density and vesicle docking at the presynaptic active zone. Neuron 69, 304-316.

Team Members Postdoctoral Fellows Norbert Babai Naila Ben Fredj Brice Bouhours Olexiy Kochubey Evan Vickers PhDStudents Ozgür Genc Enida Gjoni Elin Kronander Wei Tang Technicians Jessica Dupasquier Heather Murray Administrative Assistant Laure Dayer

BMI - Brain Mind Institute

Kochubey, O., and Schneggenburger, R. (2011). Synaptotagmin increases the dynamic range of synapses by driving Ca2+ - evoked release and by clamping a near-linear remaining Ca2+ sensor. Neuron 69: 736 - 748.

A, The calyx of Held as a multi- active zone synapse. B, C reconstruction of all vesicles (B, bottom) and of the x-y location of membrane-docked vesicles at individual active zones (C). Taken from Schneggenburger et al. 2012 with permission; see also Han et al. 2011.