Wildhaus, Switzerland

This Retreat is sponsored by:

SUK-Programm "Doktoratsprogramme" (ETH Zurich & UZH)

7th Student Retreat

PhD Program in Microbiology & Immunology (MIM)

4th – 6th September 2014

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Welcome to the 7th Student Retreat of the MIM PhD Program

Dear Participants, We hope that you will enjoy this year’s MIM retreat and will put all laboratory related trouble out of mind. Isn’t the beautiful mountainside of Switzerland just the ideal place to de-stress and unwind? With 1354m, Panorama und Gamplüt Zentrum Wildhaus is located in the center of the sunny Toggenburg and the perfect setting for great scientific discussions. The aim of the retreat is not only to improve the interaction between the different labs, but to facilitate the socialization between the various students of the MIM PhD Program. We are looking forward to your great talks and poster presentations.

Contact information In case of any questions or should a problem arise please do not hesitate to contact us in person or give us a call: Name Phone number Email address Anna Sophie Bahlmann 079 317 56 41 anna_sophie@gmx.ch Nottania Campbell 078 713 31 52 nottaniakay.campbell@usz.ch Urs Mörbe 076 712 28 14 ursmorbe@student.ethz.ch Mario Novkovic 078 861 60 94 novkovic.mario@gmail.com Marina Tusup 078 964 46 48 marina.tusup@usz.ch Tobias Wolf 078 819 94 48 tobias.wolf@irb.usi.ch

Location

Panorama und Gamplüt Zentrum Wildhaus Steinrüthistrasse Lina and Peter Koller 9658 Wildhaus/Switzerland Phone: +41 719992828 Homepage: www.gampluet.ch/index.php

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Program – Overview

time/date Thursday, 4th Friday, 5th Saturday, 6th

08:00 8:40 Departure from Zürich HB (EC) 9:48

Arrival in Buchs 10:50 Arrival in Wildhaus (bus)

Breakfast Breakfast

08:30 Student Session 3 (2 students) 09:00

HIKE & LUNCH

09:30 Coffee Break

10:00 Dr. Paul McLaren

10:30

11:00 Arrival & welcome

Student Session 4 (2 students) 11:30

12:00 12:00 Lunch 12:00 Lunch

12:30

13:00 Student Session 1 (2 students)

Dr. Steve Pascolo

13:30 Student Session 5 (3 students) 14:00

Dr. Oliver Hartley 14:30

15:00 Coffee Break

15:05 Departure from Wildhaus 17:20

Arrival in Zurich HB

15:30

Student Session 2 (4 students)

Workshop 16:00

16:30

17:00

17:30 Dr. Tobias Junt

18:00

Dinner

18:30 Dinner

19:00

19:30

Poster session 2

20:00 Poster session 1

20:30

21:00

Party

21:30

22:00

22:30

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Detailed Program

Thursday, September 4th 08:40 Departure Zurich HB 11:00 – 12:00 Arrival & welcome 12:00 – 13:00 Lunch

Lecture session I Chair: Tobias Wolf

13:00 – 13:05 Introduction of the MIM student council 13:05 – 13:35 Nottania Campbell

Reconstruction of HIV-1 full-length reference genomes from short sequence reads

13:35 – 14:05 Lucia Reh Degree of efficacy loss of broadly neutralizing antibodies during HIV-1 cell-to-cell transmission is strain and epitope dependent

14:05 – 15:05 Guest Lecture I Oliver Hartley, Prof. PhD; University of Geneva Department of Pathology and Immunology (PATIM)

Title: HIV prevention via blockade of CCR5: the ins and outs 15:05 – 15:35 Coffee Break

Lecture session II Chair: Anna Sophie Bahlmann

15:35 – 16:05 Thomas Edinger Human Cathepsin W is a host factor required for escape of influenza A virus from late endosomes

16:05 – 16:35 Mario Novkovic

Systems immunological analysis of fibroblastic reticular cells from secondary lymphoid organs

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16:35 – 17:05 Daniel Andritschke

Involvement of the actin-polymerising factor SPIRE in salmonella typhimurium infection

17:05 – 17:35 Boas Felmy Visualizing Salmonella replication in muro 17:35 – 18:35 Guest Lecture II

Tobias Junt, PhD; Novartis Institutes for Biomedical Research, Basel, Switzerland

18:30 – 19:30 Dinner 20:00 -21:30 Poster Session I (Bahlmann – Hupfeld)

Friday, September 5th

Lecture session III Chair: Mario Novkovic 08:30 – 09:00 Giorgia Brambilla Pisoni

Role of tmx1 in protein folding and in ERA-associated degradation

09:00 – 09:30 Hans Winkler Interaction of dendritic cells with food-borne nanoparticles 09:30 – 10:00 Coffee Break

Lecture session IV Chair: Nottania Campbell

10:00 – 11:00 Guest Lecture III

Paul McLaren, PhD; Ecole Polytechnique Fédérale de Lausanne Title: Impact of human genetic variation on HIV disease progression

11:00 – 11:30 Hulda Jonsdottir Novel system for analysis of coronavirus-host interactions 11:30 – 12:00 Vural Yilmaz

Pattern recognition requirements in vaccination versus immunity to infection

12:00 – 13:00 Lunch

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Lecture session V Chair: Marina Tusup

13:00 – 13:30 Guest Lecture IV

Steve Pascolo, PhD ; Department of Dermatology, University Hospital of Zürich, Zürich, Switzerland

Title: How to create a spin-off

13:30 – 14:00 Marina Sabate Bresco Immune response during bone healing in a murine fracture model with osteomyelitis: role of biomechanical stability

14:00 – 14:30 Urs Mörbe

Assessing the role of CXCL13-expressing stromal cells in lymphoid organ development

14:30 – 15:30 Coffee Break

Afternoon session 15:30 – 17:30 Workshop 18:00 – 19:30 Dinner 19:30 – 21:00 Poster Session II (Ivic – Wolf) 21:00 – ?????? Social Evening

Saturday, September 6th 09:00 – 13:30 Social event (hiking) 15:05 Departure from Wildhaus 17:20 Arrival in Zürich HB

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Guest Speakers

Oliver Hartley, PhD Position and contact details Assistant Professor Centre Médical Universitaire, Geneva, Switzerland Phone: +41 (22) 379 5475 Email: oliver.hartley@unige.ch Abstract In the continued absence of an effective HIV vaccine, over 2M new HIV infections occur every year, with over 95% of these in developing countries. Calls have been made for alternative prevention strategies, including medicines that can be used to provide protection from HIV infection during sexual intercourse. My presentation will cover our work on such an HIV prevention approach. Our strategy was inspired by the observation that people genetically deficient for the chemokine receptor CCR5, which is also the principal HIV co-receptor, are healthy but almost completely resistant to HIV. Our aim has been to recapitulate this phenotype using agents that pharmacology block CCR5, and the inhibitors we use are analogues of its natural chemokine ligands. Over the last decade we have identified and optimized several chemokine analogues with highly potent anti-HIV activity, and used them to prove the concept that topical blockade of CCR5 is sufficient to prevent mucosal transmission of HIV. Our most advanced inhibitor is about to enter a first clinical trial as a vaginal gel. The inhibitors we developed act via unusual mechanisms involving the intracellular trafficking of CCR5, and the progress we made was only possible because we were able to take account of the results of fundamental studies of CCR5 cell biology. We now have the satisfaction of beginning to pay back our debt to basic science by using the molecules we have developed as tools to provide further insights into the cell biology of CCR5 and the details of how HIV uses it to enter and infect target cells.

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Paul McLaren, PhD

Position and contact details Junior Group Leader in Bioinformatics School of Life Sciences, École Polytechnique Fédérale de Lausanne Institute of Microbiology, University Hospital and University of Lausanne Phone: +41 (0) 21 693 18 74 Email: paul.mclaren@epfl.ch Abstract Rapid expansion of genomic technologies allows an unparalleled ability to interrogate the impact of human genetic variation on disease. HIV is a unique model for studying this impact since host genetic variation influences both clinical outcome and the genetic sequence and evolution of the pathogen itself. In my talk I will summarize recent efforts in understanding the full impact of human variation on HIV disease progression and how we are using the viral genome to detect regions of genetic conflict between host and pathogen. I will also briefly discuss how we are leveraging human genetic variation data available in the public domain to generate novel hypotheses aimed at improving our understanding of HIV biology.

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Steve Pascolo, PhD Position and contact details Group leader Department of Dermatology, University Hospital of Zurich, Zurich, Switzerland Phone: +41 44 6342876 Email: steve.pascolo@usz.ch Abstract Performing research leads eventually to inventions or discoveries that can be turned into patents. Those can be licensed to companies or used as a cornerstone to create a biotechnology company stemming from University: a spin-off. By founding a company you have the advantage of creating your own carrier opportunities, keeping in touch with university research and making links to industry. As examples of possible paths, I will present the history of two different models of spin-off that I (co-) created: CureVac GmbH in 2000 and Miescher Pharma GmbH in 2008. Thereby, I will introduce the basic requirements and mechanisms that may help you setting your own company based on your (or other’s) academic research results.

Tobias Junt, PhD

Position and contact details Research Investigator Centre Médical Universitaire, Geneva, Switzerland Novartis Institutes for Biomedical Research, Basel, Switzerland Email: tobias.junt@novartis.com

Title Cessation of CCL2 blockade accelerates breast cancer metastasis and death by increasing IL-6 and angiogenesis.

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Abstracts of Participants

Involvement of the actin-polymerizing factor SPIRE in Salmonella Typhimurium infection Daniel Andritschke, Sabrina Dilling, Rosalie Heilig, Mario Emmenlauer, Pauli Rämö and Wolf-Dietrich Hardt Institute of Microbiology, ETH Zurich The enteropathogenic bacterium Salmonella Typhimurium is a common cause of gastroenteritis and can trigger pronounced mucosal inflammation. Like many other pathogenic Gram-negative bacteria, it employs a type III secretion system (TTSS) to inject effector proteins into host cells. The effectors SopE, SopE2 and SopB are injected by TTSS-1. These proteins stimulate actin rearrangement by interfering with Rho GTPase signaling. The resulting pronounced actin polymerization leads to the formation of characteristic membrane ruffles, facilitating Salmonella invasion. On the contrary, SipA directly binds to F-actin promoting local actin polymerization, filament stabilization and bundling. Recent research in our group shows that SipA efficiently mediates invasion in the absence of SopE, SopE2 and SopB. Furthermore, internalization does neither require nor induce membrane ruffling and seems to be Rho-GTPase-dependent. These results suggest a different strategy for SipA-mediated internalization compared to other effector proteins. Using a genome wide siRNA screen, we try to identify genes playing a role in this type of Salmonella invasion. Cellular components, interacting with SipA and SipA-mediated entry will be characterized using cell biology methods to eventually gain more insights into this mechanism.

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Staphylococcus aureus Small Colony Variants are induced by low pH N. Leimer*, A. S. Bahlmann*, C. Rachmühl*, M. Palheiros Marques*, A. Furrer*, M. Schwarz*, F. Andreoni*, U. Matt*, K. Seidl*, R. A. Schüpbach° and A. S. Zinkernagel* *Division of Infectious Diseases and Hospital Epidemiology °Division of Surgical Intensive Care Medicine, University Hospital of Zurich, University of Zurich, Switzerland

Objectives Staphylococcus aureus (SA) invades and persists within host cells. Its ability to survive intracellularly has been associated with the small colony variant (SCV) phenotype. SCVs are characterized by slow growth and down-regulated virulence factor expression – thus well-adapted for intracellular persistence. SA infections may relapse due to reemerging bacteria from intracellular reservoirs. We studied SCVs that evolve by cultivation of SA in growth conditions reflecting the environment in the human host. We used these conditions to screen for therapeutic strategies that help to eradicate the intracellular persisting bacteria.

Methods Host cells were infected with SA and the phenotype of recovered bacteria determined. Intracellular SA localization was determined by fluorescence microscopy. Growth conditions mimicking the acidic milieu of phagolysosomes were used to investigate the effect of low pH on SA phenotype. To investigate the potential of lysosomal alkalizing agents in SCV eradication, the number and phenotype of persisting bacteria from treated and untreated cells were compared.

Results During the course of infection, the number of intracellular surviving bacteria was reduced, but the percentage of SCVs increased. Cell imaging experiments indicated that persisting bacteria accumulated within lysosomal compartments where the pH is low. SA survived in growth medium with similar acidity (pH4.0-6.5). The percentage of bacteria manifesting the SCV phenotype increased greatly with increasing acidity. Host cells treated with agents raising intralysosomal pH showed a significant lower frequency of SCVs compared to non-treated cells.

Conclusions SA persists within host cell lysosomes and survives in low pH. The emergence of SCVs in low pH medium suggests that this phenotype is better adapted to withstand this otherwise bactericidal environment. These results indicate that alkalizing agents might help to develop therapeutic strategies that ensure complete SCV reservoir eradication.

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Impact of persistent viral infections on immune responsiveness in mice Isabel Barnstorf, Annette Oxenius Institute of Microbiology, Department of Biology, ETH Zurich, Switzerland Vaccines or microbial challenges cause immune responses caused by the various constituents of the host`s immune system, which can be altered by different kinds of modulation. For instance, steady exposure to persistent viral infections (the "virome"), the constant encounter with commensal microorganisms at mucosal surfaces (the "microbiome") and the vaccine and/or infection history represent such modulations. Persistent viral infections are well distributed among humans with approximately 8-12 infections per individual. There is only limited knowledge on how persistent viral infections affect immune responsiveness and immune homeostasis. In contrast to the "microbiome" that is progressively found to modulate immune responses. The aim of this project is to address the influence of wide-spread persistent viral infections (MCMV, LCMV) on the general composition, phenotype and function of diverse innate and adaptive immune cells in mice. In order to fill knowledge gaps concerning vaccine efficacy, susceptibility to infection by heterologous pathogens, predisposition to autoimmunity and immunological ageing.

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Innate Immune Signaling Events in Macrophages upon Adenovirus Infection Michael Bauer, Nicole Stichling, Maarit Suomalainen, Urs F. Greber Institute of Molecular Life Sciences UZH Adenovirus infection of immune cells leads to the induction of a variety of innate immune signaling events such as the release of cytokines and chemokines. While many of these factors have antiviral functions, Adenoviruses have been known to exploit some of them and thereby enhance their life cycle. Many of these factors and the events leading to inflammatory responses and pro-viral effects are still largely unknown. This project here aims to identify and characterize new cellular factors inhibiting or facilitating Adenovirus infection. To this end, we will develop a CRISPR/Cas knockout approach in nontransformed mouse macrophages which closely resemble alveolar macrophages encountered by the virus during natural infection. The aim is to screen for infection and cytokine/chemokine phenotype and correlate these results with specific aspects of antiviral immune defense. We will use confocal and high-throughput microscopy, electron microscopy, and immunoblotting in our experimental techniques. To shed further light to the mechanisms of entry and trafficking of viruses, we will employ fluorescence and whole-genome labeled Adenoviruses. The release and activation of cytokines will be evaluated with the help of a reporter gene assay. Ultimately, this work will help us gain a better understanding of the interplay between viral and host cell factors and may open up new approaches to Adenovirus-mediated gene therapy and to modulating and controlling viral infections.

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Structural and functional analysis of lipoprotein glycosylation in slow- and fast-growing mycobacteria Katja Becker, M.sc. Ph.D. student University of Zurich Institute of Medical Microbiology Gloriastr. 30/32 CH-8006 Zurich kbecker@imm.uzh.ch Lipoproteins are part of the mycobacterial cell envelope and fulfil crucial roles in cell homeostasis and virulence. Next to their lipidation, many mycobacterial lipoproteins possess glycan-moieties whose functions are mainly unknown. LppX and LpqW are two glycosylated lipoproteins involved in cell wall synthesis and virulence which will be used as a model for the about 100 lipoproteins in M. tuberculosis. While LppX functions in the transport of complex lipids across the outer membrane, LpqW determines the outer membrane composition. In this project, the glycosylation sites and motifs of these two mycobacterial proteins will be determined. The function of specific glycan-moieties on protein localization, stability and function will be elucidated by mutating glycosylation sites and by assessing the transformed bacilli in functional assays. M. smegmatis, a fast- growing, saprophytic mycobacterium, will be used to identify glycosylation sites. For functional assays however, M. tuberculosis will be mutated and analyzed as well. Virulence assays will be performed with the M. tuberculosis strains deficient for lipoprotein glycosylation at specific sites. Results obtained during this project will contribute to the general understanding of the regulation of cell wall integrity and host-pathogen interaction. Furthermore, more detailed knowledge on the structure of LppX and LpqW might open up possibilities to use these in tuberculosis vaccine design.

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Maintenance of cellular proteostasis through adaptive mechanisms regulating endoplasmic reticulum quality control and degradation machineries Timothy Jan Bergmann1,2, Fiorenza Fumagalli1,3, Maurizio Molinari1,4 1Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland 2Eidgenössische Technische Hochschule Zürich (ETHZ), 8092 Zurich, Switzerland 3Universität Bern, 3000 Bern, Switzerland 4Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, 1015 Lausanne, Switzerland e-mail of corresponding author: timothy.bergmann@irb.usi.ch Synthesis of membrane bound and secreted proteins occurs within the endoplasmic reticulum (ER). As these proteins are synthesized into the ER, their folding process is assisted by a large number of chaperones and undergoes quality control mechanisms, which allows the export into the secretory pathway of proteins that achieved their native conformation. Proteins that fail in achieving their proper conformation, are engaged by the endoplasmic reticulum associated degradation (ERAD) machinery, are retrotranslocated into the cytosol and ubiquitilated for proteosomal degradation. When a cell is subjected to an overwhelming production of proteins in the ER, it responds by specifically up-regulating transcription and translation of chaperones and ERAD components while at the same time reducing the translation of cargo proteins. This reaction, termed unfolded protein response (UPR), activates different transcriptional programs. Activation of these programs has a latency of several hours and if the cell is not able to restore proteostasis, it may lead to its death. Experimental data using inducible cell lines revealed that at low misfolded protein expression levels, the cells tolerate the ectopic protein. Above a specific threshold – which depends on the type of expressed substrate – cells do activate the UPR response which increases with increasing burden of misfolded protein. We aim to identify how cells respond to the presence of misfolded proteins within the ER and which mechanisms are involved in response to the expression of misfolded proteins below the threshold for UPR induction and how these responses differ, upon synthesis of misfolded proteins with different features.

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Asymmetric cell division and barrier function in T cell fate determination Mariana Borsa*, Annette Oxenius Laboratory of Infection Immunology, Microbiology Department, ETHZ. *maborsa@ethz.ch Activation of T lymphocytes requires the formation of an immunological synapse (IS) where a sustained interaction between the TCR with MHC complexes presenting peptides must occur. Early after activation, TCR signaling leads to polarization of TCRs, and many others molecules, including integrins and cytokine receptors toward the IS. This polarization is responsible to promote an asymmetric distribution of proteins that lasts during mitosis of activated T cells, resulting in two daughter cells with different phenotypes and fate determinations. The proximal daughter cell has increased expression of activation markers and effector molecules when compared to the distal daughter cell. This mechanism suggests that the fate of these two progenies can differ, with the proximal daughter adopting an effector cell fate and the distal daughter being destined as a memory cell. Data from other asymmetric cell division (ACD) models such as yeast and neural stem cells presented the possible contribution of diffusion barriers in establishing and maintaining asymmetry during cell division. We hypothesize that T cells also establish a diffusion barrier to regulate asymmetric partitioning of proteins to daughter cells during mitosis and that the diffusion barrier might therefore represent an important mechanism to regulate cell fate decision. Before starting to investigate the question whether or not T cells establish a diffusion barrier under mitosis, we developed an efficient method to induce asymmetric cell division (ACD) in CD8+ T lymphocytes in vitro. For that, TCR tg naïve T CD8+ cells from TCR transgenic P14 and MAXI mice (P14 mice harboring CD8 T+ cells with specificity for an immunodominant lymphocytic choriomeningitis virus (LCMV) GP-derived epitope; MAXI mice harboring CD8+ T cells with specificity for an immunodominant murine cytomegalovirus (MCMV) M38-derived epitope) were co-cultured in pre-treated Poly-L-Lysine coverslips with a dendritic cell line derived from multisystem histiocytosis (Mushi) mice previously loaded with the GP33-41 epitope of LCMV or M38316-323 epitope of MCMV, respectively. Thereafter, cells were fixed, an permeabilized before staining with specific antibodies against -tubulin, and CD8, CD25, T-bet, PKC or Scribble; proteins with known polarized distribution under ACD. Mitotic cells were selected for analysis based on the appearance of DNA and -tubulin staining. Using confocal microscopy, 30 Z stacks sections were acquired and fluorescence intensity was calculated, comparing proximal and distal poles of dividing T cells. The rate of asymmetry was comparable to previously reported findings and this stablished technique will be used for future stimulation or restimulation of CD8+ T lymphocytes. In future experiments we will address the question whether or not a diffusion barrier is involved in establishing asymmetric cell division of T cells and whether disturbing diffusion barrier formation affects T cell fate decisions in vitro or in vivo.

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Role of TMX1 in Protein Folding and in ER-Associated Degradation

Giorgia Brambilla Pisoni1,2* and Maurizio Molinari1,3 1Institute of Research in Biomedicine, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland 2ETH Zurich 3Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, 1015 Lausanne, Switzerland *Corresponding author : Giorgia Brambilla Pisoni, giorgia.brambillapisoni@irb.usi.ch The endoplasmic reticulum (ER) is the site of maturation for secretory and membrane proteins in eukaryotic cells. Native proteins are transported at their intra- or extra-cellular destination sites where they can exhibit their biological functions. Misfolded proteins are removed from the ER, retro-translocated into the cytosol and degraded by 26S proteasomes (ER-Associated Degradation, ERAD). The ER contains numerous proteins that assist folding, quality control and degradation processes. Among them, about 20 members of the protein disulfide isomerase (PDI) family, most of which have poorly defined biologic activity and substrate specificity, are essential for the formation and breakage of disulfide bonds. Here we study the biological function of TMX1, an ER membrane-associated member of the PDI family, whose active site has been found in a predominant reduced state in vivo, suggesting a reducing activity of TMX1 in the ER lumen. We determined substrates requirement for TMX1 association and consequences of TMX1-substrate mixed disulfides stabilization on folding or degradation of a series of model polypeptides ectopically expressed in cultured mammalian cells. Our results reveal that TMX1 preferentially associates with membrane-bound polypeptides. The presence of N-linked glycans is not required for TMX1 association (even though TMX1 forms a functional complex with the lectin chaperone calnexin). Moreover, TMX1 does associate (and transiently forms mixed disulfides) with both folding-competent and folding-defective proteins. This implies a possible involvement of TMX1 in folding and disposal programs occurring in the ER lumen.

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Reconstruction of HIV-1 Full-length Reference Genomes from Short Sequence Reads Nottania K. Campbell1,2*, Corinna S. Oberle1,2*, Francesca Di Giallonardo1,2, Christine Leemann1, Stefan Schmutz1, Yannick Duport1, Huldrych F. Günthard1,2*, and Karin J. Metzner1,2* 1 Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Rämistrasse 100, 8091 Zürich, Switzerland 2 Life Science Zurich Graduate School, University of Zurich, University of Zurich, 8057 Zurich, Switzerland Current methods in the evolutionary analysis of viral next-generation sequencing (NGS) data employ aligning sequence reads to a reference genome. Although practical this convention results in alignment errors due to the genetic distance between these sequences and the reference, subsequently leading to an under-/overestimation of diversity. De novo assembly as an alternative approach is especially problematic when investigating the diversity of heterogeneous viruses such as the Human Immunodeficiency Virus type 1 (HIV-1). Current assembly algorithms fail to resolve this, consequently a sophisticated workflow is needed for minimizing pseudo-diversity, so as to obtain an accurate overview of the variants present in viral populations. For this HIV-1 RNA was isolated from patients’ samples as described by F. Di Giallonardo et al. (Nucleic Acids Research. 2014). We analyzed 8 HIV-1 acutely (low diversity) and 8 HIV-1 chronically (high diversity) infected patients via Illumina-MiSeq, performed quality trimming and filtered for reads >100 bp with an average Phred score >30. These were then analyzed with three alignments methods: sequential alignment refinement to HIV-1HXB2, de novo assembly with a HIV-1HXB2 scaffold, and de novo assembly. Sequential alignment entropy ~3.3% acute, and ~4.6% chronic; de novo with HIV-1HXB2 scaffold alignment entropy: ~2.4% acute, and ~3.7% chronic. De novo assembly alone was not feasible, however, using HIV-1HXB2 genome as a scaffold for contigs ±1 round of refinement proved to be the best method for deriving accurate reference assemblies. Using our sophisticated alignment workflows we’ve generated full-length reference genomes, an essential starting point for future evolutionary analyses.

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From basics to clinics: New microencapsulated Salmonella Typhi outer membrane proteins vaccine Carreño JM1, Perez-Shibayama C1, Gil-Cruz C1, Ludewig B1 1 Institute of Immunobiology, Cantonal Hospital St. Gallen Salmonella (S.) Typhi infects 15 million persons and it kills around 200,000 every year. Outer membrane proteins C and F (OmpC and F) expressed on this pathogen are targets of human immune system during infection and induce long lasting protective antibody and T cell responses in pre-clinical studies. In this project, we will characterize the specific T cell responses against OmpC and OmpF of S. typhi at the cellular and molecular level. These studies will further allow the generation of retrogenic model systems for in vivo characterization of S. typhi-specific T cell responses. To translate these basic concepts into clinics, we will test a new preparation consisting of PLGA micro-encapsulated S. Typhi OmpC and F in a clinical phase I/II study. Currently available vaccines against this pathogen have several drawbacks as the requirement of cold-chains to be transported and limited protection against infection. We have found that porins contained in this new formulation are resistant to simulated gastric fluid (SGF), which preserves their immunogenicity after oral administration. Both safety and immunogenicity of three repeated oral doses of the vaccine and establishment of the dose required to reach approximately the level of IgA immune responses elicited by a commercially available S. Typhi vaccine will be assessed. Altogether, these studies will allow the development of an effective and reliable vaccine formulation against S. Typhi that would improve human health in endemic areas.

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Towards personalized vaccination against melanoma using viral-based vaccination ex-pressing neoantigens L. Csepregi1, S. Ring1, L. Barba2, S. Ölschläger2, O. Demaria2, M. Gilliet2, D. Speiser3, S. Kochanek4, B. Ludewig1, L. Flatz1,5 1Institute of Immunobiology, Kantonal Hospital St. Gallen, CH-9007 St. Gallen, Switzerland. 2Department of Dermatology, University Hospital CHUV, Lausanne, Switzerland. 3Ludwig Cancer Research Center, Department of Oncology, University of Lausanne, Lausanne. 4Department of Gene Therapy, University of Ulm, Ulm, Germany. 5Department of Dermatology and Allergology, Kantonal Hospital St.Gallen, CH-9007 St. Gallen, Switzerland. Correspondence to LC: lucia.csepregi@kssg.ch Melanoma is one of the most aggressive forms of cancer with an increasing incidence rate in Caucasians worldwide. However, although targeted therapies like B-RAF inhibitors showed en-couraging results the tumor usually escapes within months. Longest remissions can be achieved with adoptive transfer of in vitro expanded TILs or with CTLA-4 and PD-1 blockade. Therefore much effort is being devoted to the search for additional immunotherapeutical strate-gies to recognize and eliminate malignant cells. A major obstacle is self-tolerance against clas-sical melanoma antigens. This project aims to improve the viral-based vaccination (lymphocytic choriomeningitis and adenovirus vectors) against melanoma using recently described neoanti-gens alone or in combination with classical melanoma antigens. Castle and colleagues (1) could identify de novo somatic point mutations exclusively occurring in tumor cells by next generation sequencing exome resequencing of B16F10 murine melanoma cells. Prophylactic and therapeutic vaccination of C57BL/6 mice with recombinant viral vectors ex-pressing neoantigens will be evaluated in an experimental melanoma model using the melano-ma cell line B16F10. We will thereby study the pressure of T cells on the tumor and to which extend this leads to T cell escape mutations within the tumor evading the immune response. T cell responses will not only be assessed in PBMCs but also in primary, secondary lymphoid organs, the skin and within the tumor. Experimental immunization protocols will also include the use of immunomodulating antibodies (anti-PD-1, anti-CTLA4) or adjuvants (poly(I:C), IFA). (1) Castle et al., Exploiting the Mutanome for Tumor Vaccination, American Association for Cancer Research., 2012.

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Class and specificity of T cells against C. albicans in normal and pathological Conditions Corinne De Gregorio1, Simone Becattini1,2, Mihai Netea3, Anne Puel4, Jean Laurent Casanova5, Antonio Lanzavecchia1,2, Federica Sallusto1 1Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland; 2Institute of Microbiology, ETH Zurich, Switzerland, 3Radboud University Medical Center, Nijmegen, The Netherlands; 4Institut Imagine, Paris, France; 5The Rockefeller University, New York, USA. CD4+ Th cells are crucial players in the adaptive immune response to pathogens. Th1 cells secrete IFN-cells secrete IL-4, IL-5 and IL-13 and are essential against extracellular parasites, while Th17 cells secrete IL-17A and IL-22 and protect from fungal pathogens such as Candida albicans. We developed a high throughput cell based assay that, combined with sorting of T cell subsets and with in vitro priming assays, can provide new insights on the class and specificity of the human T cell response to pathogens. With this approach we recently demonstrated that in healthy donors memory T cells specific for C. albicans are present at high frequency in CCR6+ Th17 and Th1* subsets and at low frequency in CCR6– Th1 and Th2 subsets (Becattini et al, in preparation). Using next generation TCR Vβ sequencing, we also demonstrated that several clonotypes were present in more than one subset and, in some cases, in all subsets. We are now analyzing C. albicans-specific response in patients affected by chronic mucocutaneous (CMC) or recurrent vulvovaginal (RVVC) candidiasis, in order to evaluate the contribution of different T cell subsets to disease pathogenesis. Preliminary data in RVVC patients reveal an association between susceptibility to infection and increased frequency of C. albicans-specific Th2 cells, consistent with clinical observations of elevated IgE and Th2 cytokine levels and eosinophilic infiltration in these patients. Analysis of CMC patients show an altered distribution of C. albicans-specific T cells in memory subsets, with a high frequency of cells present in the CCR6– Th1 and Th2 subsets and a few present in the CCR6+ Th17 and Th1* subsets. These studies are expected to improve our knowledge about disease pathogenesis and may be useful for the design of novel immunotherapeutic strategies.

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Human Cathepsin W is a host factor required for escape of influenza A virus from late endosomes Thomas O. Edinger, Marie-Theres O. Pohl & Silke Stertz University of Zürich Institute of Medical Virology Winterthurerstrasse 190 8057 Zürich Switzerland Corresponding author: edinger.thomas@virology.uzh.ch Human Cathepsin W (CtsW) is a lysosomal peptidase, which was identified in a genome wide siRNA screen to be required for influenza A virus (IAV) entry1. Using a set of different siRNAs directed against human cathepsin W mRNA, we confirm that reducing protein levels results in impaired IAV entry into lung epithelial cells (A549). We observed significant reduction in viral titers after siCtsW treatment but no impact on cell viability or induction of ISGs (interferon stimulated genes). This reduction was stable over time and viral replication was not restored to control levels after more than two days infection. By dissecting the entry process of IAV into different steps, we identified the exact target step where CtsW is playing its crucial role. Using different labeling and imaging techniques, we could eliminate attachment, internalization and early endosomal trafficking as entry steps that require CtsW. In contrast, we found that late endosomal trafficking of IAV is inhibited in siCtsW treated A549 cells. Confocal imaging revealed viral particles trapped in LBPA+-(lysobisphosphatidic acid)-compartments representing late endosomes in siCtsW treated cells. To confirm this effect, we applied a fusion analysis with a dual color labeled virus to detect fusion of viral membranes with endosomal membranes. Cathepsin W knockdown cells showed a significant reduction in the number and size of fusion sites compared to control cells. These data indicate a late stage blockage of viral entry after siCtsW treatment. Current efforts aim to elucidate whether the catalytic activity of CtsW is crucial for this phenotype. 1 Human host factors required for influenza virus replication. König, R., S. Stertz et al., Nature 463:813-7

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Engineering an In Vivo Bioluminescent Reporter System for in situ imaging of HIV infection in Humanized Mice Audrey Fahrny1, 2

1 Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Rämistrasse 100, 8091 Zürich, Switzerland 2 Life Science Zurich Graduate School, University of Zurich, University of Zurich, 8057 Zurich, Switzerland audrey.fahrny@usz.ch

Despite the success of antiretroviral treatment (ART) in increasing the life expectancy and quality of HIV+ patients, it is not able to cure HIV. ART is able to suppress HIV to undetectable levels in peripheral blood, however, its interruption results inevitably in viral rebound and progressive HIV disease. The crux for the development of a cure is the presence of latently HIV+ cells; a number of cells contributing to the latent reservoir, the most important ones being CD4+ memory T‐cells. A large number of questions concerning establishment, maintenance and eradication of latency remain unanswered. Thus here we aim to generate a humanized mouse model that will permit the study of HIV latency, mechanisms that contribute to the maintenance and activation of latency and approaches to activate the latent HIV reservoir. Our model consists of human CD34+ hematopoietic progenitor cells (HPC), which are genetically modified so that they conditionally express luciferase upon HIV infection. These HPCs are transplanted into the liver of immunocompromised newborn mice, such as to obtain mice with a lymphoid system of human origin, which can thus be infected with HIV-1 and in which viral presence can be tracked by luminescence. A lentiviral vector system is used to introduce a LTR-luciferase cassette into the HPC, which should result in luciferase expression only in HIV infected HPC. Preliminary in vitro investigation of the vector system has confirmed the viability of the concept; however further optimization is presently required to increase the specificity of the system. Once our vector system yields positive results in vitro, we will rapidly translate the vector system to our in vivo humanized mouse model.

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Visualizing Salmonella replication in muro Boas Felmy, Wolf-Dietrich Hardt ETHZ HCI G 415 Vladimir-Prelog-Weg 1-5/10 8093 Zurich, Switzerland bfelmy@ethz.ch Salmonella enterica enterica serovar Typhimurium (Salmonella) can be transmitted by contaminated food and is a major cause of foodborne diseases all over the world. After ingestion, a part of the Salmonella population invades the intestinal mucosa where it induces inflammation and diarrhea. This enables Salmonella to extensively grow in the cecal lumen and outcompete the microbiota. We are interested in the first few hours after Salmonella invasion into intestinal epithelial cells. Interestingly, the in vivo doubling time of an intestinal intraepithelial Salmonella colony as revealed by intravital microscopy drastically differs from in vitro conditions, 1-5h in contrast to approx. 0.5h, respectively. On the one hand the availably of nutrients might be reduced in the Salmonella containing vacuole (SCV). This is the place where Salmonella resides inside intestinal epithelial cells. On the other hand, Salmonella is not recognized by immune defense mechanisms within the SCV. Therefore, this protected environment might be a preferable niche even with the disadvantage of slower replication. This hypothesis is further supported by the fact that Salmonella express proteins responsible for integrity of the SCV, such as SifA. Upon deletion of sifA, bacteria cannot maintain the vacuolar membrane of the SCV. Therefore, they end up in the cytosol. Here, they can access more nutrients and therefore hyper replicate but also the chance of interaction with host defense mechanisms, eliminating bacteria, is increased. Which of those mechanisms is dominating in vivo we describe using tissue plating assays, immunofluorescence of fixed tissue sections and intravital microscopy.

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The role of NK cells in host defense against systemic C. albicans infection Eva Guiducci, Eva Bär and Salomé LeibundGut-Landmann Institute of icrobiology, T u rich Email: eva.guiducci@micro.biol.ethz.ch Natural killer (NK) cells have been identified as a novel key player in innate antifungal defense. In particular, mice deficient in or depleted of NK cells are highly susceptible to systemic infection with Candida albicans : they rapidly display high fungal burden in their kidneys and they eventually succumb from infection due to strongly impaired neutrophil activity. NK cells are not able to directly sense C. albicans , but they need to be primed by DC to become fully responsive. This process is mediated via a Syk-coupled fungal recognition pathway that induces secretion of cytokines, such as IL-23, which activate NK cells and selectively induce GM-CSF. In this project, we will investigate the dynamics of the NK-cell mediated immune response during systemic candidiasis in different infected organs, with a particular focus on tissue-specific subsets of NK cells that selectively secrete GM-CSF.

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Genetic Architecture of Linear Localized Scleroderma Rebecca Higgins

USZ, Division of Dermatology

email: rhiggins@tcd.ie

Linear localized scleroderma (LLS) is a rare connective tissue disorder characterised by chronic inflammation and massive accumulation of collagen. The intense autoimmune reaction results in both hardening and thickening of the skin leading to the affected areas to cave in from atrophy. It can affect atients in areas throughout the body including arms, legs and sometimes face. The disease presents as linear lesions surrounded by healthy skin. This mosaic state is believed to create an immunological microenvironment resulting in the deleterious necrotic state. This leads to terrible disfigurement that often cannot be concealed. As of yet very little is understood about the condition in terms of both genetic and clinical aetiology. The disease is limited in treatment options and most often these treatments are unsatisfactory. The incidence of localized scleroderma in adults and children is 2.7/100’000 population per year. There is increasing evidence that that LLS might be based on genetic alterations in affected tissues. LLS usually starts in early childhood and even congenital onset has been described. There is no published inheritance pattern that would suggest a germline genetic pattern with dominant or recessive inheritance. LLS follows Blaschko’s lines, which suggests an embryological development. This suggests that LLS is based on somatic mutations that create a mosaic state as has been described in many other skin conditions. The aim of this project is to describe the genetic architecture of LLS in the hope that this could lead to a better understanding of the disease.

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From protein function to supermolecular structure: Listeria phage A511 baseplate structure and identification of receptor binding proteins Mario Hupfeld1, Ricardo Guerrero-Ferreira2, Martin Loessner1, Takashi Ishikawa3, Petr Leiman2 and Jochen Klumpp1 1Institute of Food, Nutrition and Health Schmelzbergstrasse 7, ETH Zurich, 8092 Zurich, Switzerland, 2Institut de Physique des Systèmes Biologiques, EPF Lausanne, LBBS, Lausanne, Switzerland, 3Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland For correspondence: Mario Hupfeld (mario.hupfeld@hest.ethz.ch) Our understanding of the infection of Gram-positive bacteria by phages is still incomplete. Bacteriophage A511 is a contractile-tailed, dsDNA, Myoviridae phage with a wide host range within the genus Listeria. It has been shown to be a good tool in pathogen detection especially in food products. The first steps in the infection cycle are initiated by the attachment to the surface of the bacterium. This is believed to be a two-step process, mediated by two different receptor binding proteins (RBPs). We could identify one RBP, namely Gp108, supposedly a short tail fiber protein of the phage. Here we show the results of GFP binding assays carried out for the other protein candidates that come into contact with the bacterial cell surface upon infection. These include Gp98 and Gp99 which form the central hub-like structure of the baseplate. Gp104 is similar to a putative tail fibre, although a function is not known. Gp106 represents a VrlC like protein, which has been found in a number of phages infecting both Gram-positive and Gram-negative bacteria and is considered a potential receptor binding protein of phage A511. Future experiments are aimed to further characterize these proteins. We are also developing a structural model of the A511 baseplate (in the contracted and non-contracted state) which will be based on Cryo-electron microscopy images fitted with crystallized protein structures. The expected results will elucidate the mechanisms involved in phage contraction, adsorption and subsequent viral DNA injection.

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A novel in vitro/vivo selection strategy for lentiviral vectors Sandra Ivic1, Renier Myburgh1, Karl-Heinz Krause2, Roberto F. Speck1 1Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich; University of Zurich, Zurich, Switzerland 2Dept. of Pathology and Immunology, Geneva Medical Faculty, Dept. of Genetic and Laboratory Medicine, Geneva University Hospitals, Centre Medical Universitaire, Geneva, Switzerland sandra.ivic@usz.ch Genetic engineering of hematopoietic progenitor cells (HPC) by lentiviral-based vectors suffers from their low transduction rate with ~20% when aiming a single integration event. This amount of transgene expression may not be sufficient for the correction of a number of diseases. We propose a novel in vitro/in vivo selection/suicide system based on the expression of the human reduced folate carrier 1 (hRFC1) and the human ribonucleoside-diphosphate reductase subunit M2 (RRM2). hRFC1 is the main transport protein for the uptake of folates which are indispensable for purine synthesis and therefore for DNA synthesis. A greater expression level of hRFC1 should render cell more sensitive to killing by methotrexate (suicide) but resistant against trimetrexate (selection) due to their pharmacological properties - untransduced cells are expected to show the opposite effects with higher resistance to methotrexate but lower threshold killing to trimetrexate. RRM2 catalyzes the reduction of ribonucleotides into desoxyribonucleotides and its overexpression should lead to resistance to its inhibitor hydroxyurea (selection of transduced cells). We expect an additive or even synergistic effect when trimetrexate and hydroxyurea are given together on selection/killing of transduced vs. untransduced cells. All compounds are FDA approved and thus potentially permitted for use in human. We are currently examining the concept proposed in vitro using various cell lines. Provided promising results, we then move forward to gene engineering HPC and their transplantation into humanized mice. Transduced cells would be monitored via GFP in vivo for their proliferation or disappearance depending upon the compounds administered.

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Novel system for analysis of coronavirus-host interactions Hulda R. Jonsdottir1.3, Ronald Dijkman1.3, Regulo Rodriguez2, Volker Thiel1.3 1Institute of Virology and Immunology, Bern, Switzerland 2Institute of Pathology, Cantonal Hospital St. Gallen, Switzerland 3Vetsuisse Faculty, University of Bern, Switzerland hulda.jonsdottir@vetsuisse.unibe.ch Human airway epithelium (HAE) represents the entry port of respiratory virus infection. Advances in cultivation of primary human lung epithelial cells have enabled comprehensive studies of these viruses in air-liquid-interface cultures (HAE cultures) that morphologically resemble the conducting airways in vivo. After differentiation the cultures contain different cell types such as basal, ciliated and goblet cells. Four common human CoVs (HCoV-229E, OC43, NL63 and HKU1) are detected worldwide and believed to be responsible for approximately 6% of all respiratory tract infections. Despite high incidence, knowledge of fundamental HCoV-host interactions is limited. We have shown HAE cultures to be a universal platform to study HCoV infection. However, to characterize virus-host interactions HAE cultures should be made amenable to genetic modification with lentiviruses. We show here that HAE cultures are refractory to apical and basolateral transduction. However, undifferentiated cells are readily transduced with 20-30% efficacy with low MOI. Transgene expression remains stable during differentiation and doesn’t affect cellular composition. To create highly transgenic HAE cultures the cells must be positively selected and propagated. Primary cells have a finite life-span in culture but inhibition of Rho-associated protein kinase (ROCK) induces a basal cell phenotype prolonging their life-span. Treating primary cells with this inhibitor doesn’t alter their transduction potential or their differentiation. With this inhibitor we can transduce and sort primary cells prior to establishment of modified HAE cultures. These cultures will enable detailed studies of host response to HCoV infection and gain insight into the biology of human respiratory viruses.

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USA300 methicillin-resistant Staphylococcus aureusin Zurichbetween 2001 and 2013 Kati Seidl, Nadja Leimer,Miguel Palheiros Marques, Alexandra Furrer, Gabriela Senn, Anne Holzmann-Bürgel, Ulrich Matt, Annelies S. Zinkernagel Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Switzerland

Aims To investigate the prevalence of the highly virulent and in the United States most prevalent methicillin-resistant Staphylococcus aureus(MRSA) clone USA300, at the University Hospital of Zurich.

Methods MRSA strains isolated at the University Hospital of Zurichhave been collected and PFGE typed since 1992.These strains were retrospectively compared to the PFGE pattern of the USA300 strain JE2. All isolates with a respective PFGE pattern were spa-typed and tested for the presence of the arginine catabolic mobile element (ACME)and Panton-Valentine Leucocidin (PVL)genes.

Results The first MRSA strain with a USA300 PFGE pattern was isolated in 2001 from a patient visiting from the US. It was a spa-type t008 and carried the ACME andPVL genes.The USA300 strain has represented between 0% (in 2002) and 9.2% (in 2012) of all MRSA isolates in our hospital. Various USA300 subtypes were identified based on either the PFGE pattern, the spa-type or absence of either thePVL or ACME genes. All the USA300 strains including the variants (n=47) accounted for 5.6% of all MRSA isolates that were typed between 2001 and 2013 and reached a maximum of 14.5% in 2009. They predominantly caused skin and soft tissue infections (74.4 %).

Conclusions USA300 has been present in our hospital for over twelve years. In contrast to the US it has not become the predominant MRSA clone. Strict hospital hygiene measurements are key in preventing USA300 strains from spreading in Zurich, Switzerland.

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DIAGNOSIS OF AN ENTEROVIRUS 104 STRAIN IN A LUNG TRANSPLANT RECIPIENT BY HIGH-THROUGHPUT SEQUENCING D. Lewandowska1*, M. Huber1*, M. Schuurmans2#, O. Zagordi1#, A. Zbinden1#, F. D. Geissberger1, J. Huder1, P. Schreiber3, J. Böni1, C. Benden2, N. u ller3$, A. Trkola1$ 1 Institute of Medical Virology, University of Zurich, Zurich, Switzerland 2University Hospital of Zurich, Division of Pulmonary Medicine, Zurich, Switzerland 3 University Hospital of Zurich, Division of Infectious Diseases, Zurich, Switzerland *, #, $ contributed equally Email: Lewandowska.dagmara@virology.uzh.ch Huber.Michael@virology.uzh.ch Enterovirus (EV) and Rhinovirus (RV) species can cause a wide spectrum of diseases. Precise discrimination would be of advantage for disease monitoring particularly in immunocompromised individuals, as the clinical outcome and associated risks of EV and RV infections differ. We report of a 51-year old individual with a protracted respiratory tract infection 4 months after lung transplantation for respiratory failure related to cystic fibrosis. Subsequent respiratory samples were analyzed by a commercial multiplex real-time PCR, which detects 18 different respiratory viruses. Due to cross-reactivity issues of this assay, if both EV and RV are positive, samples are recorded EV positive. RV is only scored positive in absence of EV reactivity. Following an initial RV only positivity, the subsequent series of samples proved highly positive for RV but only borderline for EV, suggesting an EV infection that is not properly detected by the kit with RV cross-reactivity or a possible dual infection with both viruses. To confirm or rule-out co-infection, we performed whole nucleic acid high-throughput sequencing of diverse clinical specimen from several time points. De novo assembly revealed infection with a Human Enterovirus C 104 (EV-104) closely related to the recently identified AK11 strain. Using reference-based alignment we recovered full-length genomes. The meta-genomic approach clearly ruled out RV as source of the highly positive PCR signal, as no RV-sequences were detected. The meta-genomic approach proved to be successful in supporting the EV diagnosis and clarifying potential viral co-infections, highlighting the potential of the technology in complex diagnostic situations.

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Assessing the role of CXCL13-expressing stromal cells in lymphoid organ development Urs Mörbe1, Lucas Onder1, Hung-Wei Cheng1, Qian Chai1, Burkhard Ludewig1 1Institute of Immunobiology, Kantonal Hospital St. Gallen, CH-9007 St. Gallen, Switzerland Correspondence to UM: ursmoerbe@student.ethz.ch The development of lymphoid organs during embryogenesis depends on the interaction between lymphoid tissue inducer cells (LTi) with lymphoid tissue organizer cells (LTo). It has been proposed that during lymph node organogenesis, mesenchymal LTo cells secrete C-XC motif chemokine 13 (CXCL13) in response to nerve-derived retinoic acid. CXCL13 subsequently triggers the attraction of CXCR5+-LTi cells, inducing a downstream signaling cascade resulting in the formation of a defined lymph node microenvironment. This work aims to target CXCL13-producing LTo cells during development and CXCL13-producing stromal cells in the adult animal in vivo and to assess their fate and function cells. For that, a CXCL13-reporter mouse was generated.

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Role of activating receptors in natural killer (NK) cell mediated restriction of lyic Eppstein Barr virus infection Anita Murer University of Zurich Institute of Experimental Immunology Winterthurerstrasse 190 CH-8057 Zürich anita.murer@uzh.ch Epstein Barr virus (EBV) infects the majority of the human adult population and persists within the host over lifetime. In most cases primary EBV infection is asymptomatic. However, acute primary EBV infection can result in infectious mononucleosis (IM) and predisposes for the development of EBV-associated classical Hodgkin lymphoma as well as multiple sclerosis. Why acute primary infection occurs in some individuals but not in others remains unclear. Recently it was shown that natural killer (NK) cells limit lytic EBV infection in vivo in mice with reconstituted human immune system components and seemingly directly recognize lytically EBV infected cells. This observation might indicate the involvement of activating NK cell receptors in the recognition of lytic infection. Indeed, two ligands of the NKG2D and DNAM-1 activating receptors on NK cells have been shown in vitro to be important in triggering the cytotoxic NK cell response towards the Akata Burkitt’s lymphoma (AKBM) cell line when undergoing lytic replication. Using RT-qPCR, the transcriptional regulation of all known NKG2D and DNAM-1 ligands on lytic and latent infected AKBM was analyzed. No difference in NKG2D ligand expression could be observed between lytic and latent infected cells on RNA level. However, our more recent findings showed differential expression of certain activating ligands on the protein level. These data suggests that ligands for activating receptors on NK cells are variably regulated on protein level in lytic versus latent infected AKBM cells.

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Systems immunological analysis of fibroblastic reticular cells from secondary lymphoid organs Mario Novkovic1, Cristina Gil-Cruz1, Christian Perez-Shibayama1, Lucas Onder1, Hung-Wei Cheng1, Elke Scandella1, Gennady Bocharov2, Burkhard Ludewig1 1 Institute of Immunobiology, Kantonal Hospital St. Gallen, St. Gallen, Switzerland 2 Institute of Numerical Mathematics, Russian Academy of Sciences, Moscow, Russia Mario.Novkovic@kssg.ch The major function of the immune system is to protect the host from infection by finding and eliminating invading pathogens. Secondary lymphoid organs (SLOs) exist mainly to facilitate efficient interactions between the immune system and foreign antigens and they are strategically positioned at routes of pathogen invasion. Lymph nodes (LNs), for example, are found at convergence points of afferent lymph vessels and morphologically they can be divided into several regions, each containing various sub-compartments with different cell populations. Similarly, Peyer’s patches (PPs) play a pivotal role in the induction of protective responses in the gut due to their localization and organization. Stromal cells, such as fibroblastic reticular cells (FRCs) in the T cell zone, contribute greatly to the induction of immune responses and general functionality of the immune system. Thus it is important to understand their structural organization, interactions with hematopoietic cells, differentiation patterns and plasticity on a cellular and molecular level, and how these affect the global systems level. Our goal will be to dissect and predict LN stromal cell behaviour in health and disease by multi-scale integration of both lower and higher level biological data. Hence, several systems immunology approaches will be applied. One such approach includes generation of histological sections of the FRC network in SLOs using the Ccl19-Cre-EYFP reporter mice, which will then be subjected to confocal microscopy and 3D reconstruction. Quantitative shape analysis will be performed in order to elucidate the global network properties as well as single-cell morphologic parameters.

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NCR1-Ligand interaction in the cross-talk between NK and T cells Katharina Pallmer, Annette Oxenius Institute of Microbiology, Department of Biology, ETH Zurich, Switzerland Previous findings have shown that virus-specific T cells which lack the ability to sense type-I Interferon are prone to be eliminated by Natural Killer (NK) cells during the early phase of Lymphocytic Choriomeningitis virus (LCMV) infection. Activated IFNAR-/- T cells are specifically recognized and killed in an Natural cytotoxicity receptor (NCR)1 dependent manner. It is assumed that IFNAR-/- T cells up-regulate NCR 1 ligands following LCMV infection and that type-I interferon blocks the up-regulation (or induces down-regulation) of NCR1 ligands in antigen-specific T cells upon activation. Thus, NCR1 activation on NK cells might besides playing an important role in regulating T cell expansion during acute infection, also be implicated in T cell regulation during chronic or non-infectious situations. We will therefore test this hypothesis in different disease models.

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Degree of efficacy loss of broadly neutralizing antibodies during HIV-1 cell-to-cell transmission is strain and epitope dependent Lucia Reh, Carsten Magnus, Merle Schanz, Jaqueline Weber, Therese Uhr, Peter Rusert, Alexandra Trkola Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich reh.lucia@virology.uzh.ch In contrast to free-virus entry, HIV-1 cell-to-cell transmission allows for a high efficacy of virus infection to which neutralizing antibodies (nAbs) and even highly potent broadly neutralizing antibodies (bnAbs) have been shown to dramatically lose neutralization potency. Since the latter are considered as main leads for vaccine design and as therapeutics for passive immunization, a precise definition of their inhibitory potential during cell-to-cell transmission is needed. To this end, we tested a range of bnAbs for their inhibitory capacity during cell-to-cell transmission of HIV-1 strains from subtypes A, B and C. Overall, the potency to inhibit HIV-1 cell-to-cell transmission was strongly decreased compared to free-virus transmission across all bnAbs tested. However, activity loss varied considerably between virus strains and high potency against free-virus did not ensure lower loss in activity during cell-to-cell transmission. Intriguingly, inhibition capacities of certain bnAb-virus combinations proved comparable for both transmission modes. Yet, this preserved activity was highly strain dependent and no bnAb that potently blocked cell-to-cell transmission over a range of HIV-1 strains could be identified. To estimate the consequences of activity loss during cell-to-cell transmission, we conducted detailed mathematical analyses that showed an increased probability of viral resistance mutations to bnAbs to arise through cell-to-cell transmission rather than free-virus spread. In sum, our data suggest that efficacy of bnAbs during cell-to-cell transmission cannot be predicted by their free-virus activity. Potent inhibition of both transmission routes will only be possible through a combination of bnAbs, either by multi-component vaccines or antibody cocktails in passive immunization.

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Tracing the origins of actin inhibitors from animals, algae, and bacteria Silke Reiter1, Reiko Ueoka1, Agustinus R. Uria1, Eric J. N. Helfrich1, Muriel Gugger2, Shigeki Matsunaga3, and Jörn Piel1 1Institut fu r ikrobiologie, idgeno ssische Technische ochschule u rich ( T ), Vladimir- Prelog-Weg 1-5/10, 8093 Zurich, Switzerland 2Institut Pasteur Collection des Cyanobacteries, Laboratoire Collection des Cyanobacteries, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France 3Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan sreiter@ethz.ch Actin inhibitors like swinholide A, tolytoxin, and rhizopodin are useful drug candidates and versatile research tools. Comparison of chemical backbones and their actin binding characteristics of various actin-inhibiting polyketides yielded interesting consistencies, even though the compounds were isolated from great variety of organisms. The intriguing mix of diverse molecular scaffolds and shared structural features of this group of small molecules is what prompted us to investigate the evolutionary origin of the biosynthetic machinery responsible for their production. Using (metha-) genomic methods paired with bioinformatic prediction and phylogenetic analysis it was not only possible to propose the biogenic pathways for three polyketide natural products but also to suggest an evolutionary scenario. Additionally, we were able to further underline the assumption that many polyketide natural products are of bacterial origin, which may live in symbiosis with larger organisms such as marine animals. The knowledge about the evolution of polyketide synthases will help efforts to design polyketides with desired properties for drug discovery using bioengineering.

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Viral-based vaccination against malignant melanoma using melanocyte-specific self-antigens S. Ring1, L. Csepregi1, L. Barba2, S. Ölschläger2, O. Demaria2, M. Gilliet2, D. Speiser3, S. Kochanek4, L. Burkhard1, L. Flatz1,5 1Institute of Immunobiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland 2Department of Dermatology, University Hospital CHUV, Lausanne, Switzerland 3Ludwig Cancer Research Center, Department of Oncology, University of Lausanne, Lausanne 4Department of Gene Therapy, University of Ulm, Ulm, Germany 5Department of Dermatology and Allergology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland Correspondence to SR: Sandra.Ring@kssg.ch Currently melanoma accounts for only 4 % of dermatological cancers but is responsible for 80-90 % of skin cancer related deaths. With the recent promising results of CTLA4 and PD-1 blockade, enhancing specific immune responses, much effort is being devoted to the search for additional immunotherapeutical strategies for successful treatments. Many tumor-associated antigens (TAAs) are nonmutated “self-antigens” which are attractive targets considering vaccine development because they are shared among tumor patients. In our project we address the feasibility of a new anti-tumor vaccination by using a recently developed vaccine vector. Our vector is a genetically modified recombinant replication-deficient LCMV expressing the melanoma-specific TAAs glycoprotein 100 (gp100) and tyrosinase-related protein-2 (Trp-2). Subcutaneous immunization of C57BL/6 mice with rLCMV-gp100 elicits a strong and long-lived antigen-specific CD8+ T-cell response. Preliminary experiments have shown that prophylactic vaccination with rLCMV-gp100 leads to a significant delay in tumor growth. In order to study the immunogenicity of our vaccine vector we will immunize different knock-out mice (e.g. MDA5-/-, TLR7-/-) to elucidate which antigen presenting cells are involved and which signaling pathway plays an important role. This knowledge is of great importance to improve the vaccination strategy. As tolerance mechanisms will render immunization in a therapeutic setting difficult we will combine our immunization with the adoptive transfer of gp100-specific T cells from TCR transgenic mice (pmel-1) into naïve C57BL/6 mice to understand what happens with the tumor/self-specific cells. Finally we will combine the use of blocking antibodies against the inhibitory receptors PD-L1 and CTLA-4 with vaccination.

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Combining antigen formulations for human vaccination against cancer ulia Ru hl, Christian u n (U ) University of Zurich Institute of Experimental Immunology Winterthurerstrasse 190 C - 0 7 u rich ruehl@immunology.uzh.ch Epstein-Barr virus (EBV) is a γ-herpesvirus that preferentially infects B cells and establishes life-long chronic infection in more than 90% of the adult human population worldwide. The infection is usually asymptomatic, but EBV is associated with a number of human malignancies such as Burkitt’s and odgkin’s lymphoma. In our studies, we target an EBV antigen to dendritic cells (DCs), because T cell responses can be enhanced through antigen delivery to endocytic receptors on DCs. Our group has previously demonstrated that targeting EBNA1 to DEC-205 elicits promising Th1-type CD4+ T cell responses in vitro and in vivo. To improve the CD8+ T cell response we aim to explore the potential of different endocytic receptors and recombinant viruses (such as lentivirus and adenovirus) towards MHC class I antigen presentation. We will target endocytic receptors such as CD141 (specific for the minor, preferentially cross-presenting DCs), CD303 (specific for plasmacytoid DCs), CD11c (present on conventional DCs), HLA class II, CD40, DC-SIGN and macrophage mannose receptor (more widely expressed on human antigen presenting cells). Because of EBVs exclusive tropism for humans, the studied model organism will be NOD-scid gamma c-/- mice with human immune system components, which develop in these mice after neonatal intrahepatic injection of human CD34+ hematopoietic progenitor cells (huNSG mice). We aim to elicit strong EBNA1 specific CD4+ and CD8+ T cell responses by combining different targeting to endocytic receptors and viral vectors in huNSG mice. We will then challenge the vaccinated mice by EBV infection and virus associated tumorigenesis.

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Immune response during bone healing in a murine fracture model with osteomyelitis: role of biomechanical stability Sabaté Brescó, Marina1,2; Kluge, Katharina2; Ziegler, Mario1; Richards, Geoff2; Moriarty, T Fintan2; O' Mahony, Liam1 1 Swiss Institute of Allergy and Asthma Research (UZH), Davos, Switzerland 2 AO Research Institute Davos, Davos, Switzerland Correspondence: Marina.Sabatebresco@aofoundation.org Introduction: Implant instability is considered a risk factor for delayed healing of fractures and infection; however, little experimental data is available confirming this belief, or describing the underlying mechanisms. In this study, a murine model was used to investigate differences in immune response in bone when fractures are fixed with rigid or non-rigid (i.e. flexible) constructs. A clinical strain of Staphylococcus epidermidis, which is one of the leading etiologic agents in orthopedic infections, was used to inoculate animals. Methods: Rigid and flexible MouseFixTM titanium plates, with or without Staphylococcus epidermidis (104 CFU) inoculation, were used to fix osteotomized C57bl/6 mouse femora. Mice (female, 20-26 weeks old) were sacrificed at 7, 14 and 30 days after surgery (n=6-9 per group). Viable bacteria were quantified from the implant, bone and soft-tissue. Bone cells were cultured and stimulated to collect supernatants for cytokine and chemokine quantification. Lymph node cells and bone cells were characterized by flow cytometry. Results: At each time-point over 30 days, unstable fractures had a higher infection rate compared to stable fractures. Macrophage lineage cells (F4/80+) increased in percentage over time in all four conditions, but slightly more in animals with flexible implants. In lymph node, CD3+CD4+IL-17+ cells were increased at early time-points in inoculated animals, especially in those where bacteria were not detected. IL-10+ and IFN-γ+ cells were similar between all groups. TNF-α, IL-10 and G-CSF were increased at day 7 in inoculated groups, especially in animals with a flexible device, while MCP-1 had a late increase.

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Candida albicans in chronic mucocutaneous candidiasis patients Franziska Schönherr1,2, Cristina Fragoso2, Orlando Petrini1,3, Salomè LeibundGut-Landmann1 1 Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland 2 Laboratory of Applied Microbiology,SUPSI,Via Mirasole 22A, 6501 Bellinzona, Switzerland 3 POLE Pharma Consulting, Breganzona, Switzerland schoenhf@ethz.ch Objectives: Chronic mucocutaneous candidiasis (CMC) is a recurrent or persistent infection ofmucosal tissues, skin and nails, caused by Candida albicans. The disease affects usually peoplewith primary immunodeficiency. To persist within the host C.albicans has to adhere and colonise host surfaces, either as a pathogen or as a commensal. We tried to characterize C. albicans isolated from patients with CMC and the reference strain SC5314. Methods: We isolated C. albicans strains from the oral cavity of 3 CMC patients and used the blood isolate SC5314 as a reference. The isolates were characterised using three microsatellite markers, to test clonality. All isolates were tested for their ability to form biofilm and an adhesion assay was carried out using epithelial cells .In addition, all isolates were tested for their ability to colonize the oral cavity in an oropharyngeal candidiasis (OPC) mice model.

Results & Conclusions: Fragment analysis demonstrated clonality of the C. albicans populations of the CMC patients. All CMC isolates adhered better to epithelial cells than the reference strain, even when they displayed a lower biofilm formation. In the OPC mouse model, CMC isolates caused a more to the tenfold higher fungal burden than the reference strain in the mice tongues. We could detect all CMC isolates even 7 days post infection this might be due to the high adherence. This might prevent the cells of getting released from the tissue and so they stay unnoticed by the immune system. In colonization adherence seems to be more important than biofilm formation.

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Characterization of the HIV-1 latent reservoir in vivo Victoria P. Strouvelle1,2, Valentina Vongrad1, Dominique L. Braun1, Karin J. Metzner1, and Huldrych F. Günthard1 1 Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, Rämistrasse 100, 8091 Zürich, Switzerland 2 Life Science Zurich Graduate School, University of Zurich, University of Zurich, 8057 Zurich, Switzerland The HIV-1 latent reservoir is a major barrier to eliminating HIV-1 as it is responsible for the persistence of HIV-1 in patients on effective antiretroviral treatment (ART) although the viral load in plasma decreases to undetectable levels. Due to this, patients have to remain on ART life-long as drug discontinuation eventually results in viral rebound from the latently infected cells. For this reason, new methods to deplete the latent reservoir are constantly being sought. Previous studies on HIV-1/HCV co-infected patients revealed a link between interferon alpha (INFα) treatment and decrease of the IV-1 latent reservoir in patients on ART. This project aims to characterise the HIV-1 latent reservoir and assess the impact of INFα/Ribavirin treatment on the IV-1 latent reservoir in a total of 30 well-documented HIV-1/HCV co-infected patients with both acute and chronic HIV-1 infection from the Swiss HIV Cohort Study (SHCS) and the Zurich Primary HIV Infection Study (ZPHI). To do this, various forms of the HIV-1 genome will be amplified and quantified by qPCR using target specific primers in cell samples from these patients. Highly sensitive qPCR assays with a 10-copy sensitivity were established to measure a broad spectrum of HIV-1 DNAs and RNAs including non-integrated DNA, unspliced, multiple- and singularly spliced mRNAs, etc., all of them markers for different stages of the HIV-1 life cycle. In addition, patients’ cells will also be assessed for their levels of replication competent, inducible viruses through the establishment of a viral outgrowth assay.

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The lifestyle of a stable L-form of Listeria monocytogenes

Patrick Studer, Titu Staubli, Markus Schuppler, and Martin J. Loessner IFNH, LFV B27, Schmelzbergstrasse 7, 8092 Zürich patrick.studer@hest.ethz.ch L-forms are cell wall-deficient variants of common bacteria that retain the capacity to proliferate in the wall-less state. They are generated in the lab by interfering with peptidoglycan synthesis followed by cultivation in osmotically stabilized media. Due to the lack of a supporting structure, L-forms display drastic physiological and morphological changes. We investigate the mode of proliferation and the lifestyle of L-forms of the Gram-positive pathogen Listeria monocytogenes. Time-lapse analysis of a stabilized, non-reverting L-form strain revealed that the cells proliferate by a completely different mechanism than their walled counterpart. They form various protrusions which finally pinch off, resulting in the release of internal and external progeny cells. Newly formed cells often remain connected to the mother cell by thin strands. These strands feature a high degree of mechanic flexibility and stability as revealed by flow cell experiments, were the strands can be stretched in length by a factor of almost three. Employing FLIP (Fluorescence Loss in Photobleaching), we observed that GFP as a marker of cytoplasmic content can be transferred between connected cells. Furthermore we verified the viability of intracellular produced vesicles by showing that vesicles isolated by micromanipulation can form new colonies. Surprisingly, all these processes happen in absence of normally essential FtsZ, thus highlighting the uncoordinated nature of L-form proliferation. L-forms and their primitive lifestyle not only allow to study basic mechanisms of bacterial cell biology, but also provide a glimpse into possible ancestral proliferation mechanisms and the evolution of cell division.

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Immunomodulation by RNA: Fundamental and translational studies

Marina Tusup1, Thomas Kündig1, Steve Pascolo1 1Department of Dermatology, University Hospital Zürich, Zürich, Switzerland Correspondence: marina.tusup@usz.ch Recombinant RNA (mRNA) is a versatile and safe vehicle for gene therapy and particularly for vaccination. Injected recombinant mRNA stimulates both innate immunity and adaptive immunity. Innate immune cells are activated mostly through the triggering of Toll Like Receptor (TLR)-3, -7 and -8, while adaptive T- and B- cells are stimulated through recognition of the antigen encoded by the mRNA. Even though naked mRNA, have been used in human clinical studies, improvements of mRNA-vaccines are being made by encapsulation of mRNA in particles using liposomes or protamine. Protamine-RNA particles of different sizes are potent TLR-inducers in vitro and thereby trigger cytokine production. Cytokines can have some anti-cancer activity on their own. Moreover, the complexation of mRNA with protamine can be used as a gene delivery system. In this work we use Protamine-RNA particles to study the potential of this product for anticancer immune therapy (eventually combined with chemotherapy) and the impact of natural RNA modifications on immunomodulation.

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Interaction of dendritic cells with food-borne nanoparticles Hans C. Winkler1, Zuzana Garajova1, Elisabeth Maria Schraner2, Cordula Hirsch4, Mark Suter3, Peter Wick4, Hanspeter Naegeli1 1Institute of Veterinary Pharmacology and Toxicology, 2Institute of Veterinary Anatomy and 3Division of Immunology, Vetsuisse Faculty, University of u rich, 0 7 u rich, Switzerland; 4Swiss Federal Laboratories for Materials Science and Technology, 9014 St. Gallen, Switzerland Consumers ingest food-borne nanoparticles (NPs) for example in the form of SiO2 (E551) or TiO2 (E171), and it is expected that new emerging nanotechnology applications will dramatically enhance oral exposure to NPs by intentional or accidental incorporation in food, beverages or supplements. This increases the urgency to characterize the interaction of NPs with the intestinal immune system because any derailment of the gut-associated immunity may precipitate immunemediated pathologies like inflammatory bowel disease. After oral uptake, NPs encounter intestinal dendritic cells, which are the key “decision makers” in the immune response as they discriminate innocuous antigens from potentially harmful pathogens. Dendritic cells avoid reactions against beneficial commensal bacteria or normal food constituents, but induce inflammatory reactions to counteract invasion by pathogens. NPs could potentially interfere with this delicate balance between tolerance and activation of intestinal immunity. Therefore, a new hazard inherent to food-borne NPs is their possible ability to interact with dendritic cells and alter their critical function in fine-tuning immunological outcomes. To test this hypothesis, food-grade NPs consisting of E171, E551 and FePO4 were incubated with dendritic cells generated from murine bone marrow using either Flt3-L (yielding different subsets of naïve steady-state dendritic cells) or GM-CSF (yielding inflammatory dendritic cells). The endpoints analyzed include cellular uptake demonstrated by transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDX), dendritic cell viability, release of pro-inflammatory cytokines (IL1β, IL6, IL12, IL2 and IFN-α,) determined by immunoassays as well as dendritic cell maturation assessed by changes of the surface marker repertoire (up-regulation of CD40, CD69, CD86; down-regulation of CD62L) upon flow cytometry analysis. Interestingly, food-grade NPs (E551) induced distinctive and dose-related activation patterns in steady-state dendritic cells with a dependency on their size or surface area. A cytokine cocktail containing GM-CSF and IL3 further enhances this response of dendritic cells. Instead, steadystate dendritic cells are refractory to NPs consisting of E171 or FePO4. These findings support the hypothesis that specific NPs may interfere with the function of the gut-associated immune system and our in vitro assay provides a screening system to test whether NPs considered as food ingredients or food contact materials are able to activate naïve steady-state dendritic cells.

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The Migrome of T cells Tobias Wolf 1,2, J. Rieckmann3, C. Basso1, F. Meissner3, M. Mann3, F. Sallusto1, A. Lanzavecchia1,2, R. Geiger1,2

1Institute for Research in Biomedicine (IRB), Bellinzona, Switzerland 2Institute of Microbiology, ETH Zurich, Switzerland 3Max Planck Institute of Biochemistry, Munich, Germany Naïve T cells, which are stimulated by an antigen, undergo an extensive cascade of proliferation and differentiation. The expression of several proteins that determine the migratory behavior of naïve T cells changes shortly after activation. Consequently, naïve T cells differ from activated ones in their coordinated migration. While naïve T cells predominantly recirculate from the blood through secondary lymphoid organs, activated T cells are frequently found in antigen-rich lymphoid and non-lymphoid tissues. To systematically analyze the temporal changes of the T cell proteome after activation we use high-resolution mass spectrometry. We followed the abundance of 7’ 16 proteins in primary human naïve CD4+ T cells during an activation time course of four days. The expression of proteins involved in migration to non-lymphoid tissues, such as integrins, remained steady early after activation and started to increase 72 h after activation. At this time point T cells start to leave lymph nodes in vivo and traffic to tissues. As such we hypothesized that we may identify novel proteins required for T cell migration by focusing on the ones that display a similar kinetic expression as integrins. In addition, we aim at performing an shRNA screen to detect genes, when knocked down, increase or decrease the migratory capacity of T cells. Our final list of candidate proteins will be followed up in detail with respect to their role in migration, using transwell and microscopical assays to analyze the migration phenotype. Interesting candidates will be further analyzed in mouse models. Generally, recent advances in DNA sequencing technologies and proteomics led to an almost complete picture of the gene and protein landscape in a cell. However, the function of a large fraction of proteins is still unknown. As such our systematic analysis of proteins that are involved in migration – the migrome - will be an important step towards the global understanding of the cell. The migrome may also lead to new insights into how to tailor the T cell response for immunotherapy.

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Pattern recognition requirements in vaccination versus immunity to infection Vural Yilmaz, Annette Oxenius and Roman Spörri ETH Zürich Institute of Microbiology HCI G 403 Vladimir-Prelog-Weg 1-5/10 8093 Zürich E-Mail: yilmazv@ethz.ch The induction of adaptive immunity is crucially dependent on innate activation signals that convert resting antigen-presenting cells (APCs) into immunogenic ones. APCs expressing the relevant innate pattern recognition receptors can be directly activated by pathogen-associated molecular patterns (PAMPs) to become competent to prime T-cell responses. Alternatively, APCs can be activated indirectly by proinflammatory mediators synthesized by PAMP-exposed cells. Yet such indirectly activated APCs fail to prime effector CD4+ and CD8+ T cell responses against vaccines. This lead to the conclusion that direct pattern recognition is required for the successful priming of adaptive immunity. However, recent data from experiments with pulmonary influenza infection challenges this conclusion. There, IL-1R signalling on APCs replaces direct pattern recognition in promoting CD8+ T cell responses, but not CD4+ T cell responses. The present project aims to shed light on the differential requirement for direct pattern recognition in vaccination versus immunity to infection. We are particularly interested firstly, in the requirement for pattern recognition in the context of cross-presentation, secondly, in surrogate activation mechanisms where the presenting APCs do not express the appropriate pattern recognition receptors, and thirdly, the basis for the differential requirement for direct pattern recognition in the priming of CD4+ and CD8+ T cell responses to influenza infection.

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Poster Sessions I (Bahlmann-Hupfeld)

1) Anna Sophie Bahlmann Staphylococcus aureus Small Colony Variants are induced by low pH

2) Isabel Barnstorf Impact of persistent viral infections on immune responsiveness in mice

3) Michael Bauer Innate Immune Signaling Events in Macrophages upon Adenovirus Infection

4) Katja Becker Structural and functional analysis of lipoprotein glycosylation in slow- and fast-growing mycobacteria

5) Timothy Bergmann Maintenance of cellular proteostasis through adaptive mechanisms regulating endoplasmic reticulum quality control and degradation machineries

6) Mariana Borsa Asymmetric cell division and barrier function in T cell fate determination

7) Juan Manuel Carreno

From basics to clinics: New microencapsulated Salmonella Typhi outer membrane proteins vaccine

8) Lucia Csepregi Towards personalized vaccination against melanoma using viral-based vaccination ex-pressing neoantigens

9) Corinne De Gregorio Class and specificity of T cells against C. albicans in normal and pathological Conditions

10) Audrey Fahrny Engineering an In Vivo Bioluminescent Reporter System for in situ imaging of HIV infection in Humanized Mice

11) Eva Guiducci The role of NK cells in host defense against systemic C. albicans infection

12) Rebecca Higgins Genetic Architecture of Linear Localized Scleroderma

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13) Mario Hupfeld From protein function to supermolecular structure: Listeria phage A511 baseplate structure and identification of receptor binding proteins

Poster Session II (Ivic – Wolf)

14) Sandra Ivic A novel in vitro/vivo selection strategy for lentiviral vectors

15) Nadja Leimer

USA300 methicillin-resistant Staphylococcus aureusin Zurichbetween 2001 and 2013

16) Dagmara Lewandowska DIAGNOSIS OF AN ENTEROVIRUS 104 STRAIN IN A LUNG TRANSPLANT RECIPIENT BY HIGH-THROUGHPUT SEQUENCING

17) Anita Murer Role of activating receptors in natural killer (NK) cell mediated restriction of lyic Eppstein Barr virus infection

18) Katharina Pallmer NCR1-Ligand interaction in the cross-talk between NK and T cells

19) Silke Reiter Tracing the origins of actin inhibitors from animals, algae, and bacteria

20) Sandra Ring Viral-based vaccination against malignant melanoma using melanocyte-specific self-antigens

21) Julia Rühl Combining antigen formulations for human vaccination against cancer

22) Franziska Schönherr

Candida albicans in Chronic mucocutaneous candidiasis patients 23) Victoria Strouvelle

Characterisation of the HIV-1 latent reservoir in vivo

24) Patrick Studer The lifestyle of a stable L-form of Listeria monocytogenes

25) Marina Tusup Immunomodulation by RNA: Fundamental and translational studies

26) Tobias Wolf The Migrome of T cells

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Participants Name Institute Email address Andritschke, Daniel

ETH, Microbiology daniel.andritschke@micro.biol.ethz.ch

Bahlmann, Anna Sophie

UZH, University Hospital of Zurich: Division of Infectious Diseases and Hospital Epidemiology

anna_sophie@gmx.ch

Barnstorf, Isabel

ETH, Microbiology isabelba@ethz.ch

Bauer, Michael UZH, Institute of Molecular Life Science

michael.bauer@uzh.ch

Becker, Katja UZH, Medical Microbiology

kbecker@imm.uzh.ch

Bergmann, Timothy

ETH, Institute for Research in Biomedicine Bellinzona

timothy.bergmann@irb.usi.ch

Borsa, Mariana ETH, Microbiology maborsa@ethz.ch Brambilla Pisoni, Giorgia

ETH, Institute for Research in Biomedicine Bellinzona

giorgia.brambillapisoni@irb.usi.ch

Campbell, Nottania

UZH, University Hospital of Zurich: Division of Infectious Diseases and Hospital Epidemiology

nottaniakay.campbell@usz.ch

Carreno, Juan Manuel

ETH, Cantonal Spital St. Gallen

juancar@student.ethz.ch

Csepregi, Lucia UZH, Cantonal Spital St. Gallen

lucia.csepregi@web.de

De Gregorio, Corinne

ETH, Institute for Research in Biomedicine Bellinzona

degregoriocorinne@gmail.com

Edinger, Thomas

UZH, Institute of Medical Virology

ede-thomas@gmx.de

Fahrny, Audrey UZH, University Hospital of Zurich: Division of Infectious Diseases and Hospital Epidemiology

audrey.fahrny@usz.ch

Felmy, Boas ETH, Institute for Microbiology and Immunology

bfelmy@ethz.ch

Guiducci, Eva ETH, Microbiology eva.guiducci@micro.biol.ethz.ch

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Higgins, Rebecca

University Hospital rhiggins@tcd.ie

Hupfeld, Mario ETH, INFH mario.hupfeld@hest.ethz.ch Ivic, Sandra UZH, University

Hospital of Zurich: Division of Infectious Diseases and Hospital Epidemiology

sandra.ivic@usz.ch

Jonsdottir, Hulda

UniBE, Institute of Virology and Immunology

hulda.jonsdottir@vetsuisse.unibe.ch

Leimer, Nadja UZH, University Hospital of Zurich: Division of Infectious Diseases and Hospital Epidemiology

nadja.leimer@usz.ch

Lewandowska, Dagmara

UZH, Institute of Medical Virology

lewandoska.dagmara@virology.uzh.ch

Mörbe, Urs ETH, Cantonal Spital St. Gallen

ursmoerbe@web.de

Murer, Anita UZH, Experimental Immunology

murer@immunology.uzh.ch

Novkovic, Mario

ETH, Cantonal Spital St. Gallen

novkovic.mario@gmail.com

Pallmer, Katharina

ETH, Microbiology pallmerk@ethz.ch

Reh, Lucia UZH, Institute of Medical Virology

luciareh@gmx.de

Reiter, Silke ETH, Microbiology sreiter@ethz.ch Ring, Sandra UZH, Cantonal Spital

St. Gallen sandra.ring@gmx.de

Rühl, Julia UZH, Experimental Immunology

ruehl@immunology.uzh.ch

Sabate Bresco, Marina

ETH, SIAF/AO Research Institute

msabatebresco@gmail.com

Schönherr, Franziska

ETH, Microbiology schoenhf@ethz.ch

Strouvelle, Victoria

UZH, University Hospital of Zurich: Division of Infectious Diseases and Hospital Epidemiology

victoria.strouvelle@usz.ch

Studer, Patrick ETH, Institute of Food, Nutrition and Health

patrick.studer@hest.ethz.ch

Tusup, Marina UZH, University Hospital: Department of Dermatology

marina.tusup@usz.ch

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Winkler, Hans UZH, Institute of Pharmacology and Toxicology

hans.winkler@vetpharm.uzh.ch

Wolf, Tobias ETH, Institute for Research in Biomedicine Bellinzona

tobias.wolf@irb.usi.ch

Yilmaz, Vural ETH, Microbiology yilmazv@ethz.ch