2015-11 list of erc nrf sa.pdf

8/17/2019 2015-11 List of ERC NRF SA.pdf

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Evaluation Panel: LS1 - Molecular and Structural

Project ID: Acronym: 309509

Principal Investigator: Dr. Chirlmin Joo [email protected]

RNAI Biology and Biochemistry

Host Institution: TECHNISCHE UNIVERSITEIT DELFT, DELFT, NLwww.tudelft.nl

Unveiling the Molecular Basis of RNA Interference with Single Molecule Fluorescence

Recent groundbreaking discoveries have changed our view on RNA from that of a passive informationcarrier to an important regulatory element. MicroRNA is a small regulatory RNA that controls nearly allmRNAs in eukaryotic cells. Since this regulation process (termed RNA interference/RNAi) occurs in asequence-specific manner, we can manipulate gene expression using custom-designed small RNAs. This

remarkable discovery introduced the possibility of RNA-based gene therapy and triggered intensiveresearch on the RNA-induced silencing complex (RISC), the core machinery of RNAi. The molecularmechanism of RISC is, however, poorly understood due to the limited spatial and temporal resolutionof traditional tools, which has deterred development of an RNAi assay applicable to medical sciences. Iwill use single-molecule fluorescence to investigate the entire process of RISC action with high spatio-temporal resolution. From ‘RISC assembly’ through ‘tar get mRNA search’ to ‘target mRNAdegradation ,’ it requires the cooperative action of multiple RISC components. As the protein-proteinand protein-RNA interactions are dynamic processes, it is challenging to study them in bulk where theinteractions are diffusion-limited and subsequent processes are masked from observation. With single-molecule microscopy, I will observe all the processes in real time and quantitatively examine thekinetics. In addition, I will dissect the complex processes of RISC action by observing multiple RISCcomponents simultaneously, using multicolor FRET that I have developed. Furthermore, to elucidatethe complex nature of RNAi, I will reconstitute protein complexes with a single-moleculeimmunoprecipitation technique that I have recently innovated. This first single-molecule study on RISCwill enable us to reveal novel molecular mechanisms of RNAi. The fruitful outcome will aid thedevelopment of RNAi free from off-target interactions, which will lead to RNAi-based gene therapy inthe near future.

End Date:

31/8/2017

mailto:[email protected]://www.tudelft.nl/http://www.tudelft.nl/mailto:[email protected]


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Project ID: Acronym: 310930 NUCLEARACTIN

Biology and Biochemistry Principal Investigator: Dr. Maria Kristina Vartiainen

[email protected] Institution: HELSINGIN YLIOPISTO, HELSINGIN YLIOPISTO, FI

http://www.helsinki.fi/university/

Actin as the Master Organizer of Nuclear Structure and Function

Unlike previously thought the nucleus is a highly compartmentalized organelle. Both the genome andprocesses associated with it show non-random distribution within the nucleus. Thiscompartmentalization has a fundamental impact on nuclear processes. However, the mechanismsdriving this organization are poorly understood. I hypothesize that actin plays a key role in this

process. Nevertheless, the true potential of nuclear actin has not been fully appreciated, due to twofundamental open questions in this field, namely 1) what is the biological significance of nuclear actinand 2) what is the molecular mechanism by which actin operates in the nucleus? I intend to addressthese key questions by manipulating actin specifically in the nucleus, and by identifying nuclear actinbinding partners, respectively. My lab has recently identified the nuclear import mechanism for actin,which offers us a unique tool to manipulate nuclear actin. We will therefore create cell lines withdecreased/increased nuclear actin, and analyze the consequences by using cell biological and geneexpression tools, combined with deep sequencing. This will disclose the genes that depend on actin fortheir expression, and reveal the biological significance of nuclear actin in organizing the general nuclearlandscape. To unravel the mechanisms by which actin functions in the nucleus, we will implement anovel multi-readout, fluorescence microscopy screen to identify nuclear actin binding proteins, whichwill be analyzed by different biochemical methods. This approach will reveal how actin is connected tonuclear machineries, and what biochemical features of actin are required to power the essentialnuclear processes. These techniques will significantly broaden our understanding on the nuclearfunctions of actin, and thus likely reveal molecular mechanisms that regulate nuclear organization,which are highly relevant to basic biological processes, such as cell differentiation and epigenetics.

End Date:31/10/2017

mailto:[email protected]://www.helsinki.fi/university/http://www.helsinki.fi/university/mailto:[email protected]


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Project ID: Acronym: 311318 PROTDYN2FUNCTION

Biology and Biochemistry Principal Investigator: Dr. Paul Schanda

[email protected] A L ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES,

Host Institution: GRENOBLE, FRwww.cea.fr

Functional protein dynamics studied by solution- and solid-state NMR spectroscopy

Proteins are highly flexible objects that perform their functions by sampling a wide range ofconformations. The characterization of such motions is, therefore, crucial to establish the link between

protein structure and function. In this project we will use advanced nuclear magnetic resonance insolution state and solid state to characterize functionally important motions in two challenging classesof proteins. The first target of these studies will be a large molecular chaperone of close to 1MDa insize. Conformational changes and dynamics are a prerequisite for the function of this assembly, as itbinds, encloses and folds unfolded substrate proteins. Atomic-resolution structures of such largeobjects frozen in their crystal lattice do not provide access to dynamic information nor insight into thefolding process itself. Here, we will exploit the complementary advantages of solid- and solution-stateNMR spectroscopy to probe the dynamics, allostery and binding in a ≈1MDa object. Furthermore, wewill study how the chaperone cage influences folding, by observing in real time and at atomicresolution how substrate proteins achieve their native fold inside and outside this large molecular

edifice. We will furthermore study the mechanism of substrate translocation across membranes bycharacterizing structure, interactions and dynamics in a solute carrier protein. The dynamics of integralmembrane proteins is currently poorly understood. This relates to the need to address membraneprotein dynamics in an environment that closely resembles the native membrane. NMR techniques onproteoliposomes as well as nanodiscs are uniquely suited to get insight into native dynamics. We willuse such techniques to relate the process of substrate translocation to inherent protein dynamics overa wide range of time scales. The development of novel NMR methods will be an integral part of thesestudies, and will allow us to probe protein motion at unprecedented detail.

End Date:31/3/2018

mailto:[email protected]://www.cea.fr/http://www.cea.fr/mailto:[email protected]


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Project ID: Acronym: 335439 ABDESIGN

Biology and Biochemistry Principal Investigator: Dr. Sarel-Jacob Fleishman

[email protected] Institution: WEIZMANN INSTITUTE OF SCIENCE, REHOVOT, IL

www.weizmann.ac.il

Computational design of novel protein function in antibodies

We propose to elucidate the structural design principles of naturally occurring antibodycomplementarity-determining regions (CDRs) and to computationally design novel antibody functions.Antibodies represent the most versatile known system for molecular recognition. Research has yieldedmany insights into antibody design principles and promising biotechnological and pharmaceutical

applications. Still, our understanding of how CDRs encode specific loop conformations lags far behindour understanding of structure-function relationships in non-immunological scaffolds. Thus, design ofantibodies from first principles has not been demonstrated. We propose a computational-experimentalstrategy to address this challenge. We will: (a) characterize the design principles and sequenceelements that rigidify antibody CDRs. Natural antibody loops will be subjected to computationalmodeling, crystallography, and a combined in vitro evolution and deep-sequencing approach to isolatesequence features that rigidify loop backbones; (b) develop a novel computational-design strategy,which uses the >1000 solved structures of antibodies deposited in structure databases to realisticallymodel CDRs and design them to recognize proteins that have not been co-crystallized with antibodies.For example, we will design novel antibodies targeting insulin, for which clinically useful diagnostics areneeded. By accessing much larger sequence/structure spaces than are available to natural immune-system repertoires and experimental methods, computational antibody design could produce higher-specificity and higher-affinity binders, even to challenging targets; and (c) develop new strategies toprogram conformational change in CDRs, generating, e.g., the first allosteric antibodies. These willallow targeting, in principle, of any molecule, potentially revolutionizing how antibodies are generatedfor research and medicine, providing new insights on the design principles of protein functional sites.

End Date:31/8/2018

mailto:[email protected]://www.weizmann.ac.il/http://www.weizmann.ac.il/mailto:[email protected]


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Project ID: Acronym: 337116 TRXN-PURGE

Biology and Biochemistry Principal Investigator: Dr. Tokameh Mahmoudi

[email protected] Institution: ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM, ROTTERDAM, NL

www.erasmusmc.nl

Mechanisms of transcription in HIV latency; novel strategies to activate

The persistence of a transcriptionally competent but latent HIV infected memory CD4+T cell reservoir,despite the effectiveness of Highly Active Antiretroviral therapy (HAART) against active virus, presentsthe main impediment to HIV eradication. A novel concept in HIV eradication is to activate latent virusto subsequently eliminate with HAART. Much effort has gone into identification of protein complexes

that regulate HIV LTR activity. Strategies have mainly relied on candidate approaches. However, due totechnical limitations, comprehensive unbiased identification of host proteins associated with andnecessary for silencing of the latent HIV LTR has not been possible. Trxn-PURGE proposes a novelmultidisciplinary approach combining current knowledge of HIV transcription and new insights intoeradication strategies with state of the art high though-put approaches, mycology, virology, geneticsand conventional biochemistry to identify novel players in maintenance and activation of HIVtranscriptional latency. We will: 1. Use a novel unbiased strategy to identify the in vivo latent LTR-bound protein complex directly from infected T cells. 2. Conduct a cell-based high-throughput Haploidgenetic screen to identify novel factors essential for maintenance of HIV latency. 3. Having identifiedthree putative activators from a limited library, we will perform a large-scale screen with unbiasedlibrary of fungal supernatants to identify molecules capable of activation of latent HIV. These parallelapproaches will identify novel molecular targets and molecules in activation of HIV transcriptionallatency, which we will functionally and mechanistically characterize alone and in synergy with knowncompounds implicated in latent LTR activation in both 4. T cell lines and 5. primary human CD4+T cellsharboring latent HIV. By unravelling its molecular mechanisms, Trxn-PURGE will set the stage for thedevelopment of a clinical combinatorial therapy to activate latent HIV.

End Date:31/1/2019

mailto:[email protected]://www.erasmusmc.nl/http://www.erasmusmc.nl/mailto:[email protected]


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Project ID: Acronym: 339367 NCB-TNT

Biology and Biochemistry Principal Investigator: Prof. James Henderson Naismith

[email protected] UNIVERSITY COURT OF THE UNIVERSITY OF ST ANDREWS, ST ANDREWS,

Host Institution: UKwww.st-andrews.ac.uk

New chemical biology for tailoring novel therapeutics

Most of our drugs derive from natural products, many more natural products possess biological activitybut our inability to synthesise novel analogues hampers our ability to use them either as tools ormedicines. Cyclic peptides are common structural motifs in natural products and medicines

(vancomycin, gramicidin). They are widely recognised to constitute a promising and still underexploitedclass of molecule for novel therapeutics; specifically an important role for cyclic peptides in theinhibition of protein-protein interactions has been demonstrated. We will harness the power of therecently identified macrocyclases from the ribosomally-derived cyanobactin superfamily to preparediverse modified cyclic peptides. These enzymes exhibit the remarkable ability to macrocycliseunactivated peptide substrates. Different members of this family of macrocyclases process peptidesinto macrocycles containing from six up to twenty residues. We have characterised and re-engineeredone member of the family (PatG) which makes eight residue macrocycles. We will determine thestructural and biochemical features of the macrocyclases that are known to lead to six or to twentyresidue macrocycles. We will use these insights to put these enzymes to work in novel chemicalreactions. We will combine macrocyclases with other enzymes from the cyanobactin biosyntheticpathways (whose structures and mechanism we have largely determined) and work on solid phasepeptide substrates. By bringing together the power of solid phase methods (split and pool) and thenovel chemistry enabled by the enzymes, we will generate highly diverse macrocyclic scaffoldscontaining amino acids, enzymatically modified amino acids, non-natural amino acids and non-aminoacid building blocks. Successful completion of the project will revolutionise the design of cyclic peptide-inspired libraries with diverse backbone scaffolds for applications in target identification, drugdiscovery and tool screening.

End Date:28/2/2019

mailto:[email protected]://www.st-andrews.ac.uk/http://www.st-andrews.ac.uk/mailto:[email protected]


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Principal Investigator: Prof. Jernej Ule [email protected]

TRANSLATE Biology and Biochemistry

Host Institution: UNIVERSITY COLLEGE LONDON, LONDON, UKhttp://www.ucl.ac.uk

Specificity of translational control during unfolded protein response

Unfolded protein response (UPR) is activated by multiple types of cellular stress, and can promoteeither cell survival or apoptosis. The balance between these opposing outcomes is delicately regulated,and when lost, contributes to diverse diseases. UPR enables cells to halt general translation, whileinducing translation and transcription of specific mRNAs that escape repression. Even though the

general machinery controlling translation is well understood, several fundamental open questionsremain: 1) how are mRNAs selected for translation during UPR, 2) what role does mRNA structure andsequence play in this selection, 3) what role does UPR pathway play in the highly differentiated cells,such as neurons? My lab employs an integrative approach to understand how RNA-binding proteins(RBPs) control specific mRNAs. We recently developed hiCLIP, a method that globally quantifiesinteractions between RBPs and double-stranded RNA in live cells. Our preliminary findingsdemonstrate that a double-stranded RBP binds to structured motifs in mRNAs to control stress-inducedtranslation. I propose to determine how combinatorial recognition of RNA sequence and structure byRBPs controls mRNA localisation, stability and translation during UPR. In addition, we will assess therole of UPR pathway in neuronal differentiation. Taken together, this study aims to elucidate how cellsselect specific mRNAs for translation, and thereby survive during stress or respond to signals thatcontrol differentiation.

End Date:28/2/2019

mailto:[email protected]://www.ucl.ac.uk/http://www.ucl.ac.uk/mailto:[email protected]


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Project ID: Acronym: 647474 NeuroInCellNMR

Biology and Biochemistry Principal Investigator: Dr. Philipp Selenko

[email protected] Institution: FORSCHUNGSVERBUND BERLIN E.V., BERLIN, DE

www.fv-berlin.de

In-cell NMR monitoring of alpha-Synuclein aggregation in neuronal cells

Intracellular aggregation of the human amyloid protein alpha-synuclein is causally involved inParkinson’s disease, a debilitating neurodegenerative disorder. The goal of this project is to combinelow-resolution, fluorescence-imaging methods with high-resolution in-cell NMR and EPR spectroscopytechniques to derive macroscopic and microscopic insights into alpha-synuclein aggregate structures

directly in neuronal cells. To achieve this goal, we will employ different sets of cultured neurons andinvestigate intracellular alpha-synuclein aggregation under defined conditions of mitochondrialdysfunction and cellular oxidative stress, two of the most common denominators of the disease.Importantly, we will also establish a human stem cell model for studying alpha-synuclein aggregationwith high-resolution in-cell NMR and EPR methods, by using induced pluripotent stem cell (iPSC)derived dopaminergic neurons from Parkinson ’s disease patients and control individuals. Results fromthis study will provide novel insights into the native mechanisms of intracellular aggregate formationand ultimately enable novel pharmacological approaches for therapeutic intervention.

End Date:31/10/2020

mailto:[email protected]://www.fv-berlin.de/http://www.fv-berlin.de/mailto:[email protected]


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Evaluation Panel: LS2 - Genetics, Genomics, Project ID: Acronym:

309831 PATHOPROT Bioinformatics and Systems Biology

Principal Investigator: Dr. Anders Johan Malmström [email protected]

Host Institution: LUNDS UNIVERSITET, LUND, SEwww.lu.se

In vivo pathogen proteome profiling using selected reaction monitoring

Bacterial infections represent a major and global health problem, which is further aggravated by therapid and ongoing increase in antibiotic resistance. The limited success in the development of targetedtherapies for particular invasive strains can be attributed to our limited knowledge how pathogens

modulate their proteome homeostasis in vivo, knowledge that has so far remained elusive due totechnical limitations. Here I propose the use of proteome-wide selected reaction monitoring massspectrometry (SRM-MS) for pathogen proteome profiling from samples obtained directly from in vivousing group A streptococci (GAS) as a model system. The proposal describes the use of SRM-MS tofacilitate the construction of comprehensive and quantitative molecular anatomy knowledge modelsoutlining spatial organization, pathway organization, absolute protein concentration estimations andinteraction partners with host for complete microbial proteomes. Using the molecular anatomy asbenchmark I intend compare how the proteome homeostasis is controlled in pathogens isolateddirectly from patients with different degree of disease severity to understand how disease severity,anatomical location and host dependencies effects the proteome homeostasis. The outlined proposal

describes a generic strategy to provide comprehensive understanding of the pathogen adaptiondirectly in vivo and represents a paradigm shift in the field of bacterial infectious disease. This proposaladdresses central aspects within the medical microbiology field that has been long sought for but neverstudied due to technology limitations and will influence the development of the next generationtargeted vaccine and therapeutic development programs.

End Date:30/4/2018

mailto:[email protected]://www.lu.se/http://www.lu.se/mailto:[email protected]


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310325 NONCODEVOL Bioinformatics and Systems Biology

Principal Investigator: Dr. Juan Antonio Gabaldón Estevan [email protected]

Host Institution: FUNDACIO CENTRE DE REGULACIO GENOMICA, BARCELONA, ESwww.crg.es

Evolutionary genomics of long, non-coding RNAs

Recent genomics analyses have facilitated the discovery of a novel major class of stable transcripts,now called long non-coding RNAs (lncRNAs). A growing number of analyses have implicated lncRNAs inthe regulation of gene expression, dosage compensation and imprinting, and there is increasing

evidence suggesting the involvement of lncRNAs in various diseases such as cancer. Despite recentadvances, however, the role of the large majority of lncRNAs remains unknown and there is currentdebate on what fraction of lncRNAs may just represent transcriptional noise. Moreover, despite agrowing number of lncRNAs catalogues for diverse model species, we lack a proper understanding ofhow these molecules evolve across genomes. Evolutionary analyses of protein-coding genes haveproved tremendously useful in elucidating functional relationships and in understanding how theprocesses in which they are involved are shaped during evolution. Similar insights may be expectedfrom a proper evolutionary characterization of lncRNAs, although the lack of proper tools and basicknowledge of underlying evolutionary mechanisms are a sizable challenge. Here, I propose to combinestate-of-the-art computational and sequencing techniques in order to elucidate what evolutionary

mechanisms are shaping this enigmatic component of eukaryotic genomes.The first goal is to enablelarge-scale phylogenomic analyses of lncRNAs by developing, for these molecules, methodologies thatare now standard in the evolutionary analysis of protein-coding genes. The second goal is to explore, athigh levels of resolution, the evolutionary dynamics of lncRNAs across selected eukaryotic groups forwhich novel genome-wide data will be produced experimentally using recently developed sequencingtechniques that enable obtaining genome-wide footprints of RNA secondary structure. Finally, thisdataset will be used to test the impact on lncRNAs evolution of processes known to be important inprotein-coding genes.

End Date:31/12/2017

mailto:[email protected]://www.crg.es/http://www.crg.es/mailto:[email protected]


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310765 MACMODEL Bioinformatics and Systems Biology

Principal Investigator: Dr. Eugene Berezikov [email protected]

Host Institution: ACADEMISCH ZIEKENHUIS GRONINGEN, GRONINGEN, NLwww.umcg.nl

Harvesting the power of a new model organism: stem cells, regeneration and ageing in Macrostomum lignano

The ‘stem-cell theory ’ of ageing posits that the functional decline in adult stem cells is one of thefactors contributing to ageing. Importantly, the number of stem cells does not diminish with age in

many tissues but rather there are intrinsic and extrinsic changes that affect their functionality. Is itpossible to reverse these changes? Experiments in the emerging model Macrostomum lignano suggestthat this is indeed the case. Remarkably, induced regeneration in this animal leads to extendedlifespan: repeated amputation, followed by regeneration, results in animals that live far beyond themedian lifespan of 205 days. Regeneration in M. lignano is facilitated by stem cells called neoblasts,and it appears that regeneration resets the ‘ageing program’ in these animals. Due to its highregeneration capacity, small size, transparency and clear morphology, ease of culture, short generationtime and amenability to genetic manipulation, M. lignano has great potential as a model organism forstem cell research. I have recently started developing genomic and genetic tools and resources for thismodel, and at present my group has generated a draft genome assembly, produced de novo

transcriptome assembly, discovered several neoblast marker genes and made the first stabletransgenic lines in this animal. Here I propose to study molecular mechanisms underlying rejuvenationin M. lignano, and to further advance M. lignano as a model organism through development of missinggenetic tools and resources. I will address how young, aged and regenerated worms differ in their geneand small RNA expression profiles, and what are the differences and variation levels between neoblastsof young, old and regenerated animals. The biological roles of the identified candidate genes and theireffects on the lifespan and neoblast activity will be investigated. In parallel, methods for efficienttransgenesis and gene manipulation will be developed, and the genome annotation improved.

End Date:31/10/2017

mailto:[email protected]://www.umcg.nl/http://www.umcg.nl/mailto:[email protected]


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311000 AGELESS Bioinformatics and Systems Biology

Principal Investigator: Dr. Emma Teeling [email protected] COLLEGE DUBLIN, NATIONAL UNIVERSITY OF IRELAND, DUBLIN,

Host Institution: DUBLIN, IEwww.ucd.ie

C ompar ativ e g enomi cs / ‘w il dl i fe ’ tr ans cr i ptomi cs unc ov er s t he m ec hani sms ofhal ted ageing i n

mammals

Ageing is the gradual and irreversible breakdown of living systems associated with the advancement oftime, which leads to an increase in vulnerability and eventual mortality. Despite recent advances inageing research, the intrinsic complexity of the ageing process has prevented a full understanding ofthis process, therefore, ageing remains a grand challenge in contemporary biology. In AGELESS, we willtackle this challenge by uncovering the molecular mechanisms of halted ageing in a unique modelsystem, the bats. Bats are the longest-lived mammals relative to their body size, and defy the ‘ra te-of-living’ theories as they use twice as much the energy as other species of considerable size, but live farlonger. This suggests that bats have some underlying mechanisms that may explain their exceptionallongevity. In AGELESS, we will identify the molecular mechanisms that enable mammals to achieveextraordinary longevity, using state-of-the-art comparative genomic methodologies focused on bats.

We will identify, using population transcriptomics and telomere/mtDNA genomics, the molecularchanges that occur in an ageing wild population of bats to uncover how bats ‘age’ so slowly comparedwith other mammals. In silico whole genome analyses, field based ageing transcriptomic data, mtDNAand telomeric studies will be integrated and analysed using a networks approach, to ascertain howthese systems interact to halt ageing. For the first time, we will be able to utilize the diversity seenwithin nature to identify key molecular targets and regions that regulate and control ageing inmammals. AGELESS will provide a deeper understanding of the causal mechanisms of ageing,potentially uncovering the crucial molecular pathways that can be modified to halt, alleviate andperhaps even reverse this process in man.

End Date:31/12/2017

mailto:[email protected]://www.ucd.ie/http://www.ucd.ie/mailto:[email protected]


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648039 DUB-DECODE Bioinformatics and Systems Biology

Principal Investigator: Dr. Chuna Ram Choudhary [email protected]

Host Institution: KOBENHAVNS UNIVERSITET, COPENHAGEN, DKwww.ku.dk

Systematic Decoding of Deubiquitylase-Regulated Signaling Networks

Cellular processes are largely governed by sophisticated protein posttranslational modification (PTM)-dependent signaling networks, and a systematic understanding of regulatory PTM-based networks is akey goal in modern biology. Ubiquitin is a small, evolutionarily conserved signaling protein that acts as

a PTM after being covalently conjugated to other proteins. Reversible ubiquitylation forms the mostversatile and largest eukaryote-exclusive signaling system, and regulates the stability and function ofalmost all proteins in cells. Deubiquitylases (DUBs) are ubiquitin-specific proteases that removesubstrate-conjugated ubiquitin, and thereby regulate virtually all ubiquitylation-dependent signaling.Because of their central role in ubiquitin signaling, DUBs have essential functions in mammalianphysiology and development, and the dysregulated expression and mutation of DUBs is frequentlyassociated with human diseases. Despite their vital functions, very little is known about the proteinsand ubiquitylation sites that are regulated by DUBs and this knowledge gap is hampering ourunderstanding of the molecular mechanisms by which DUBs control diverse biological processes.Recently, we developed a mass spectrometry-based proteomics approach that allowed unbiased and

site-specific quantification of ubiquitylation on a systems-wide scale. Here we propose tocomprehensively investigate DUB-regulated ubiquitin signaling in human cells. We will integrateinterdisciplinary approaches to develop next-generation cell models and innovative proteomictechnologies to systematically decode DUB function in human cells. This will enable a novel anddetailed understanding of DUB-regulated signaling networks, and open up new avenues for furtherresearch into the mechanisms and biological functions of ubiquitylation and of ubiquitin-like modifiers.

End Date:30/9/2020

mailto:[email protected]://www.ku.dk/http://www.ku.dk/mailto:[email protected]


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Evaluation Panel: LS3 - Cellular and

Project ID: Acronym: 294523 WNTEXPORT

Developmental Biology Principal Investigator: Dr. Jean-Paul B.B. Vincent

[email protected] RESEARCH COUNCIL/THE FRANCIS CRICK INSTITUTE LIMITED,

Host Institution: SWINDON/LONDON, UKwww.mrc.ac.uk/www.crick.ac.uk

Sorting processes that ensure short and long-range action of Wnts in developing epithelia

Wnts are signaling proteins that act both at short and long range in developing tissues. Severalproteins, such as Wntless, are specifically devoted to Wnt secretion, indicating that Wnts may follow adistinct secretory route. Moreover, Wnts carry two lipid modifications, which are likely to interfere

with diffusion in the extracellular space. Much of our work will focus on the trafficking of Wingless (themain Drosophila Wnt), which forms a concentration gradient in wing imaginal discs. To chart the routetaken by Wingless from the ER to responding cells, we will devise techniques (e.g. BirA-dependent invivo biotinylation) to pulse label endogenously expressed Wingless in the secretory pathway and at thecell surface. Wingless routing will also be investigated in conditions that alter Evi/Wntless trafficking.We will capitalize on our observation that Wingless and Wntless are present on exosomes inconditioned medium. These exosomes will be purified and characterized by mass spectrometry and theresulting information will be used to devise rigorous functional assays. Similar approaches will be usedto identify and characterize proteins that associate with soluble Wingless, which is also present inconditioned medium. Our proposed approaches will also enable us to assess, for the first time, thefunction of exosomes in an intact animal. Once secreted, Wingless and associated proteins spread inthe extracellular space while remaining associated with the epithelial surface. We will use singlemolecule imaging in a reconstituted system along with mathematical modeling to test the hypothesisthat the glypican-Wnt interaction is sufficiently strong to ensure surface retention while allowingdiffusion in two dimensions. Finally we will use biochemical approaches and molecular genetics inDrosophila and mice to investigate the mode of action of Notum, a glypican-modifying enzyme thatcould be relevant to the progression of Wnt signaling dependent cancers.

End Date:

30/6/2017

mailto:[email protected]://www.mrc.ac.uk/www.crick.ac.ukhttp://www.mrc.ac.uk/www.crick.ac.ukmailto:[email protected]


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Project ID: Acronym: 322699 THE FUSION MACHINE

Developmental Biology Principal Investigator: Prof. Manfred Lindau

[email protected] PLANCK GESELLSCHAFT ZUR FOERDERUNG DER WISSENSCHAFTEN E.V.,

Host Institution: GÖTTINGEN, DEwww.mpg.de

The nanomechanical mechanism of exocytotic fusion pore formation

Cells release neurotransmitters, hormones and other compounds stored in secretory vesicles by aprocess called exocytosis. In this process, the molecules are released upon stimulation by ananomachine forming a fusion pore that connects the vesicular lumen to the extracellular space.

Similar fusion events are also essential for intracellular transport mechanisms and virus-induced fusion.Here I propose a multidisciplinary approach using highly innovative techniques to determine thenanomechanical mechanism of fusion pore formation. The proposal is based on the hypothesis that thevesicle fusion nanomachine is formed by the mechanical interactions of the SNARE proteinssynaptobrevin, syntaxin, and SNAP-25 and that the fusion pore is opened by intra-membranemovement of the transmembrane domains. I will combine fluorescence resonance energy transfermicroscopy with detection of individual fusion events using microfabricated electrochemical detectorarrays to demonstrate that fusion pore formation is produced directly by a conformational change inthe SNARE complex. I will estimate the energies that are needed to pull the synaptobrevin C terminusinto the hydrophobic membrane core and the forces that are generated by the SNARE complex for wildtype and a set of specific mutations using molecular dynamics simulations. I will determine how theseenergies and forces relate to inhibition and facilitation of experimentally observed fusion, performingpatch clamp capacitance measurements of vesicle fusion in chromaffin cells expressing wild type andmutated SNARE proteins. Based on these results I will develop a detailed picture of the molecularsteps, the energies, and the forces exerted by the molecular nanomachine of fusion pore formationand will ultimately generate a molecular movie of this fundamental biological process. Understandingcellular and viral fusion events will likely lead to novel treatments from spasms and neurodegenerationto cancer and infectious disease

End Date:31/3/2018

mailto:[email protected]://www.mpg.de/http://www.mpg.de/mailto:[email protected]


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Project ID: Acronym: 323052 SYMDEV

Developmental Biology Principal Investigator: Prof. Yrjö Helariutta

[email protected] CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF

Host Institution: CAMBRIDGE, CAMBRIDGE, UKwww.cam.ac.uk

The role of symplastic communication during root development

The symplastic route composed of plasmodesmata (PD) channels and the transporting phloem tissue(rich in PD) is the major pathway for carbon allocation in plants. How the symplastic transport route isformed during plant ontogeny and what is its significance in conducting and distributing morhogenetic

signals to the growing organs is poorly understood at the moment and is addressed here. Mylaboratory has recently made a breakthrough that facilitates the analysis of symplastic communication.In a genetic screen we identified gain-of-function mutations in a locus that codes for a CALLOSESYNTHASE isoform CALS3. The cals3-d mutations result in restricted symplastic trafficking through thePD. Using the cals3-d mutations in a vector system that allows cell type specific and inducible control ofexpression of the transgene, icals3m, we have been able to construct a molecular tool, with which wecan regulate the passage of the various signaling molecules between the neighboring cells. This toolhas already opened several new lines of research on symplastic communication concerningunderstanding of the regulation of PD channels, phloem development and symplastically movingsignals. By a combination of experimental approaches at molecular, genetic, imaging and theoreticallylevels we will investigate here: (1) How is symplastic trafficking regulated? (2) What are the(symplastic) signals specifying phloem development? (3) How do the signals emanating from thephloem control root development? (4) Can we predict new regulatory factors controlling symplastictrafficking in space and time, based on the experimental data (on the distribution of symplasticchannels, symplastically controlled genes and symplastically mobile molecules)?

End Date:31/5/2018

mailto:[email protected]://www.cam.ac.uk/http://www.cam.ac.uk/mailto:[email protected]


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Principal Investigator: Dr. Bruno Goud

MYODYN Developmental Biology

[email protected] Institution: INSTITUT CURIE, PARIS, FR

www.curie.fr

Myosins and the dynamics of intracellular membranes

Myosins are fascinating proteins with unique biochemical and physical properties. The multiple rolesthat they play in the dynamics of intracellular membranes are only beginning to emerge. Recentfindings from the research team have highlighted unexpected roles in membrane deformation and inmembrane fission played by two myosins (myosin 1b and myosin II) functioning at the interface

between the Golgi, TGN (Trans-Golgi Network) and endosomes. Building on these results, we proposeto establish a comprehensive model describing how several myosins work in concert with F-actin andwith microtubule-based motors for sustaining transport events and membrane dynamics in a region ofthe cell at the crossroads of complex trafficking pathways. Towards this general objective, our maingoals are: Goal 1: to understand the role of myosin 1b in membrane deformation Goal 2: to understandthe role of nonmuscle myosin II in membrane fission Goal 3: to characterize the actin structuresrequired for myosin functions Goal 4: to identify and to characterize other myosins functioning at theGolgi/TGN/endosome interface and to investigate their functional coordination Goal 5: to understandhow myosins are functionally coordinated with microtubule-based motors. The function of myosins willbe studied both at the cellular and physical level using two main original methodological approachesavailable to the research team: minimal in vitro assays (giant liposomes and membrane nanotubes) andnormalized cell systems (micropatterns). This proposal represents a new development in the activity ofthe research team composed of cell biologists, experimental and theoretical physicists. Success of thisproposal will rely on the strong experience of cross-disciplinary approaches that allowed the researchteam in the past to elucidate several physical mechanisms underlying transport processes andmembrane dynamics.

End Date:31/1/2019

mailto:[email protected]://www.curie.fr/http://www.curie.fr/mailto:[email protected]


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Project ID: Acronym: 637530 REPROWORM

Developmental Biology Principal Investigator: Dr. Baris Tursun

[email protected] FUR MOLEKULARE MEDIZIN IN DER HELMHOLTZ-

Host Institution: GEMEINSCHAFT, BERLIN, DEwww.mdc-berlin.de

Safeguarding Cell Identities: Mechanisms Counteracting Cell Fate Reprogramming

Regenerating tissues by reprogramming cells has the potential to become a therapeutic approach forreplacing lost tissues in patients suffering from injury or degenerative diseases such as Alzheimer ’s orMuscular Dystrophy. Strategies to generate required tissues using embryonic stem cells or induced

pluripotent stem cells (iPSCs) are associated with either ethical or medical safety issues. An alternativestrategy is to directly reprogram cells to the required tissue type by forced expression of cell fate-inducing transcription factors (TFs). Direct reprogramming (DR) has the potential to circumvent unsafeproliferative pluripotent cell stages and it allows in vivo procedures. However to date, DR is successfulin only a few cell types and it is not well understood why most cells are refractory to DR. Recently, weprovided evidence that inhibitory mechanisms play an important role in restricting cell fate conversion.We identified factors inhibiting direct conversion of germ cells into specific neurons or muscle cells.Additionally, preliminary studies in our group revealed other factors that inhibit ectopic cell fateinduction in somatic cells. The objective of this proposal is to further understand mechanisms thatrestrict DR. We aim to identify and characterize factors involved in safeguarding differentiated cells andthereby counteract induction of ectopic fates in different cells. We use C. elegans as an in vivo modeland apply large-scale forward and reverse genetic screenings with high-throughput. Next generationsequencing, tissue-specific biochemistry (ChIP-seq, SILAC) and 4D imaging will be used to elucidate themolecular function of identified DR-regulating factors. Finally, we will test the ability to convert cells inaged animals and assess the effects of ageing on the ability to induce ectopic cell fates. Our researchhas the potential to facilitate the generation of specific tissues from different cellular contexts forfuture biomedical approaches.

End Date:

29/2/2020

mailto:[email protected]://www.mdc-berlin.de/http://www.mdc-berlin.de/mailto:[email protected]


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Project ID: Acronym: 639234 PROCELLDEATH

Developmental Biology Principal Investigator: Prof. Moritz Karl Nowack

[email protected] Institution: VIB, GHENT, BE

www.vib.be

Unraveling the regulatory network of developmental programmed cell death in plants

Programmed cell death (PCD) is a fundamental biological process that actively terminates a c ell’s vitalfunctions by a well-ordered sequence of events. In both animals and plants, various types of PCD arecrucial for development, health, and the responses to various stresses. Despite their importance, onlylittle is known about PCD processes and their molecular control in plants. Still, an intricate regulatory

network must exist that renders specific plant cell types competent to initiate and execute PCD atprecisely determined developmental stages. I recently established a powerful developmental PCDmodel system in Arabidopsis thaliana, based on a PCD process occurring during root cap development.This root cap model has the potential to revolutionize existing concepts of plant PCD, as it combines aprecisely predictable PCD process in easily accessible cells on the root periphery with the abundance ofresources available for Arabidopsis research. Exploiting the root cap system will enable me to tackleunresolved fundamental questions about the regulation of developmental PCD in plants: How do cellsacquire PCD competency during differentiation? Which signals trigger PCD execution at just the rightmoment? What are the actual mechanisms that disrupt the vital functions of a plant cell? I will obtainanswers to these questions through a comprehensive strategy combining complementary approaches,taking advantage of cell-type specific transcriptomics, forward and reverse genetics, advanced live-cellimaging, biochemistry, and computational modeling. Our unpublished data point to the existence of acommon core mechanism controlling PCD not only in the root cap, but also in other vital organsincluding the vasculature, anthers, or developing seeds. Thus, this project will not only be significant toadvance our knowledge on PCD as a general developmental mechanism in plants, but also to generatenew leads to tap the so far underexploited potential of PCD in agriculture.

End Date:31/3/2020

mailto:[email protected]://www.vib.be/http://www.vib.be/mailto:[email protected]


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Project ID: Acronym: 647186 MolCellTissMech

Developmental Biology Principal Investigator: Dr. Guillaume Thomas Charras

[email protected] Institution: UNIVERSITY COLLEGE LONDON, LONDON, UK

http://www.ucl.ac.uk

Molecular and cellular determinants of cell monolayer mechanics

Epithelial monolayers are amongst the simplest tissues in the body, yet they play fundamental roles inadult organisms where they separate the internal environment from the external environment and indevelopment when the intrinsic forces generated by cells within the monolayer drive tissuemorphogenesis. The mechanics of these simple tissues is dictated by the cytoskeletal and adhesive

proteins that interface the constituent cells into a tissue-scale mechanical syncitium. Mutations inthese proteins lead to diseases with fragilised epithelia. However, a quantitative understanding of howsubcellular structures govern monolayer mechanics, how cells sense their mechanical environment andwhat mechanical forces participate in tissue morphogenesis is lacking.To overcome these challenges,my lab devised a new technique to study the mechanics of load-bearing monolayers under well-controlled mechanical conditions while allowing imaging at subcellular, cellular and tissue resolutions.Using this instrument, my proposal aims to understand the molecular determinants of monolayermechanics as well as the cellular behaviours that drive tissue morphogenesis. I will focus on fourobjectives: 1) discover the molecular determinants of monolayer mechanics, 2) characterise monolayermechanics, 3) dissect how tension is sensed by monolayers, and 4) investigate the biophysics ofindividual cell behaviours participating in tissue morphogenesis.Together these studies will enable usto understand how monolayer mechanics is affected by changes in single cell behaviour, subcellularorganisation, and molecular turnover. This multi-scale characterisation of monolayer mechanics will setthe stage for new theoretical descriptions of living tissues involving both molecular-scale phenomena(cytoskeletal turnover, contractility, and protein unfolding) operating on short time-scales andrearrangements due to cell-scale phenomena (cell intercalation, cell division) acting on longer times.

End Date:31/8/2020

mailto:[email protected]://www.ucl.ac.uk/http://www.ucl.ac.uk/mailto:[email protected]


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Project ID: Acronym: 649024 RegEvolve

Developmental Biology Principal Investigator: Dr. Jochen Christian Rink

[email protected] PLANCK GESELLSCHAFT ZUR FOERDERUNG DER WISSENSCHAFTEN E.V.,

Host Institution: DRESDEN, DEwww.mpg.de

Comparative analysis of planarian regeneration - why some worms r eg ener ate w hi l e other sdon ’t

The ability to regenerate lost body parts is widespread amongst animals, yet humans, for example, canonly regenerate specific organs. Why some animals regenerate while others hardly do remains a

fascinating conundrum, especially so in face of “survival of the fittest”. Even amongst planarianflatworms, famous for their ability to regenerate from random tissue fragments, species exist that havecompletely lost the ability to regenerate. This proposal will exploit the unique diversity of planarianregenerative abilities amongst to ask why some worms regenerate while others do not. We and othershave established that planarian Wnt signalling acts as critical node in the evolution of regenerationdefects. Using this finding as strategic focus for comparisons between regenerating and non-regenerating species, we will investigate i) the cell biological mechanisms that shape Wnt pathwayactivity; ii) the genomic mechanisms that differentially deploy critical pathway regulators; and iii)evolutionary mechanisms in form of life history trait trade-offs as possible driving force behind the driftof regenerative abilities. Key to the project is a diverse collection of regenerating and regeneration-

deficient species that my lab has established. Focused comparisons between our two primary modelspecies D. lacteum and S. mediterranea, employing pan-planarian antibodies and functional genomics,will allow us to understand the detailed causes of altered pathway activity. Comparisons amongst theentire collection of 50 species will provide the necessary breadth for identifying and studying theevolutionary principles that “naturally select” regeneration-deficient planarians. The comparativeapproach of RegEvolve will thus uniquely bridge the proximate (molecular)- with the ultimate(evolutionary) causes of regeneration defects and such interdisciplinary endeavour between molecularand evolutionary regeneration research will lead to new and profound insights into both fields.

End Date:30/9/2020

mailto:[email protected]://www.mpg.de/http://www.mpg.de/mailto:[email protected]


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Project ID: Acronym: 671083 ACTOMYOSIN RING

Developmental Biology Principal Investigator: Prof. Mohan Balasubramanian

[email protected] Institution: THE UNIVERSITY OF WARWICK, COVENTRY, UK

www.warwick.ac.uk

Understanding Cytokinetic Actomyosin Ring Assembly Through Genetic Code Expansion, Click Chemistry, DNA origami, and in vitro Reconstitution

The mechanism of cell division is conserved in many eukaryotes, from yeast to man. A contractile ringof filamentous actin and myosin II motors generates the force to bisect a mother cell into twodaughters. The actomyosin ring is among the most complex cellular machines, comprising over 150

proteins. Understanding how these proteins organize themselves into a functional ring withappropriate contractile properties remains one of the great challenges in cell biology. Efforts togenerate a comprehensive understanding of the mechanism of actomyosin ring assembly have beenhampered by the lack of structural information on the arrangement of actin, myosin II, and actinmodulators in the ring in its native state. Fundamental questions such as how actin filaments areassembled and organized into a ring remain actively debated. This project will investigate key issuespertaining to cytokinesis in the fission yeast Schizosaccharomyces pombe, which divides employing anactomyosin based contractile ring, using the methods of genetics, biochemistry, cellular imaging, DNAorigami, genetic code expansion, and click chemistry. Specifically, we will (1) attempt to visualize actinfilament assembly in live cells expressing fluorescent actin generated through synthetic biologicalapproaches, including genetic code expansion and click chemistry (2) decipher actin filament polarity inthe actomyosin ring using total internal reflection fluorescence microscopy of labelled dimeric andmultimeric myosins V and VI generated through DNA origami approaches (3) address when, where,and how actin filaments for cytokinesis are assembled and organized into a ring and (4) reconstituteactin filament and functional actomyosin ring assembly in permeabilized spheroplasts and insupported bilayers. Success in the project will provide major insight into the mechanism of actomyosinring assembly and illuminate principles behind cytoskeletal self-organization.

End Date:

31/10/2020

mailto:[email protected]://www.warwick.ac.uk/http://www.warwick.ac.uk/mailto:[email protected]


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Evaluation Panel: LS4 - Physiology, Project ID: Acronym:

309322 TUMORGAN Pathophysiology and Endocrinology

Principal Investigator: Dr. Jan Kristian Pietras [email protected]

Host Institution: LUNDS UNIVERSITET, LUND, SEwww.lu.se

Exploring the tumor as a communicating organ

The failure to bring about major advances in cancer care over the past decades points to the need for arevolution in our view of cancer as a disease caused by a lack of growth control in malignant cells. Wepropose that a tumor should be considered a communicating organ made of multiple cell types that

collectively evolve into a clinically manifested and deadly disease. With this proposition follows thattargeting of communication within tumors to attenuate the support from the stroma is the only viablestrategy to achieve long term therapeutic benefit. Our research addresses the need to study thecellular context of cancer with a higher resolution. The general aim of the proposed work is to identifysubsets of different cell types within the tumor stroma that hold utility as therapeutic targets andbiomarkers. The work will be performed through a set of experiments bridging basic biology, pre-clinical studies and molecular oncology. The specific aims are: 1) Identification of cellular subsets ofthe tumor vasculature 2) Investigation of the therapeutic utility of cellular subsets of the tumorvasculature 3) Exploration of the potential of cellular subsets of the tumor vasculature as biomarkersThe aims of the study will be pursued through a series of methodological refinements. Firstly,

identification of novel components of tumors will be achieved by the assembly of a mouse genetic toolbox enabling isolation, lineage tracing and functional studies. Secondly, single cell transcriptomesequencing will be performed to identify cellular subsets using materials from both mouse and man.Thirdly, the utility as therapeutic targets of the new cellular subsets will be assessed using a liveimaging approach. Fourthly, the clinical significance of the new cellular subsets will be investigatedusing exclusive patient materials. Taken together, the information provided by our studies will enableus to take cancer therapy into a new era of personalized medicine.

End Date:

28/2/2018

mailto:[email protected]://www.lu.se/http://www.lu.se/mailto:[email protected]


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311082 AGEINGSTEMCELLFATE Pathophysiology and Endocrinology

Principal Investigator: Dr. Tim Julius Schulz [email protected] INSTITUT FUER ERNAEHRUNGSFORSCHUNG POTSDAM

Host Institution: REHBRUCKE, NUTHETAL, DEwww.dife.de

The Role of Ectopic Adipocyte Progenitors in Age-related Stem Cell Dysfunction, Systemic Inflammation, and Metabolic Disease

Ageing is accompanied by ectopic white adipose tissue depositions in skeletal muscle and other

anatomical locations, such as brown adipose tissue and the bone marrow. Ectopic fat accrualcontributes to organ dysfunction, systemic insulin resistance, and other perturbations that have beenimplicated in metabolic diseases. This research proposal aims to identify the regulatory cues thatcontrol the development of ectopic progenitor cells that give rise to this type of fat. It is hypothesizedthat an age-related dysfunction of the stem cell niche leads to an imbalance between (1) tissue-specificstem cells and (2) fibroblast-like, primarily adipogenic progenitors that reside within many tissues.Novel methodologies that assess stem/progenitor cell characteristics on the single cell level will becombined with animal models of lineage tracing to determine the developmental origin of theseadipogenic progenitors and processes that regulate their function. Notch signalling is a key signallingpathway that relies on direct physical interaction to control stem cell fate. It is proposed that impaired

Notch activity contributes to the phenotypical shift of precursor cell distribution in aged tissues. Lastly,the role of the stem cell niche in ectopic adipocyte progenitor formation will be analyzed. Externalsignals originating from the surrounding niche cells regulate the developmental fate of stem cells.Secreted factors and their role in the formation of ectopic adipocyte precursors during senescence willbe identified using a combination of biochemical and systems biology approaches. Accomplishment ofthese studies will help to understand the basic processes of stem cell ageing and identify mechanismsof age-related functional decline in tissue regeneration. By targeting the population of tissue-residentadipogenic progenitor cells, therapeutic strategies could be developed to counteract metaboliccomplications associated with the ageing process.

End Date:28/2/2018

mailto:[email protected]://www.dife.de/http://www.dife.de/mailto:[email protected]


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311549 CALMIRS Pathophysiology and Endocrinology

Principal Investigator: Prof. Leon Johannes De Windt [email protected]

Host Institution: UNIVERSITEIT MAASTRICHT, MAASTRICHT, NLhttp://www.maastrichtuniversity.nl

RNA-based regulation of signal transduction – Regulation of calcineurin/NFAT signaling by microRNA-based mechanisms

Heart failure is a serious clinical disorder that represents the primary cause of hospitalization and deathin Europe and the United States. There is a dire need for new paradigms and therapeutic approaches

for treatment of this devastating disease. The heart responds to mechanical load and variousextracellular stimuli by hypertrophic growth and sustained pathological hypertrophy is a major clinicalpredictor of heart failure. A variety of stress-responsive signaling pathways promote cardiachypertrophy, but the precise mechanisms that link these pathways to cardiac disease are onlybeginning to be unveiled. Signal transduction is traditionally concentrated on the protein coding part ofthe genome, but it is now appreciated that the protein coding part of the genome only constitutes1.5% of the genome. RNA based mechanisms may provide a more complete understanding of thefundamentals of cellular signaling. As a proof-of-principle, we focus on a principal hypertrophicsignaling cascade, cardiac calcineurin/NFAT signaling. Here we will establish that microRNAs areintimately interwoven with this signaling cascade, influence signaling strength by unexpected upstream

mechanisms. Secondly, we will firmly establish that microRNA target genes critically contribute togenesis of heart failure. Third, the surprising stability of circulating microRNAs has opened thepossibility to develop the next generation of biomarkers and provide unexpected mechanisms howgenetic information is transported between cells in multicellular organs and fascilitate inter-cellularcommunication. Finally, microRNA-based therapeutic silencing is remarkably powerful and offersopportunities to specifically intervene in pathological signaling as the next generation heart failuretherapeutics. CALMIRS aims to mine the wealth of these RNA mechanisms to enable the developmentof next generation RNA based signal transduction biology, with surprising new diagnostic andtherapeutic opportunities.

End Date:31/1/2018

mailto:[email protected]://www.maastrichtuniversity.nl/http://www.maastrichtuniversity.nl/mailto:[email protected]


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322977 WAYS Pathophysiology and Endocrinology

Principal Investigator: Prof. Adriana Caterina Elvira Maggi [email protected]

Host Institution: UNIVERSITA DEGLI STUDI DI MILANO, MILANO, ITwww.unimi.it

Role of Liver Estrogen Receptor in female Energy Metabolism, Reproduction and Aging: What About Your Liver Sexual Functions?

In mammals, the liver is the peripheral integrator of nutrient availability and energetic needs of theentire organism. We recently demonstrated that dietary amino acids (AA) activate liver Estrogen

Receptors (ER) and that, in case of food scarcity, the lowered circulating AA decrease liver ER activityand reduce IGF-1 synthesis with the consequent blockage of the estrous cycle. Here, we hypothesizethat in females liver ERa is also a sensor of the endogenous signalling induced by transitions amongreproductive stages and a key organizer for the changes required to adapt energy metabolism toreproductive necessities. Thus, we propose that in mammals liver ERa is regulated by reproductivefunctions and that, in case of ovary malfunctioning, the altered estrogenic signalling causes metabolicimpairment leading to local and perhaps systemic disruption of energy homeostasis. To demonstrateour theory, we will explore: i) the molecular pathways activating liver ERa and the related ERatranscriptome by genome-wide analytical tools; ii) the hepatic metabolism and the systemicconsequences of liver ER pharmacological and genetic manipulations by means of metabolomic

technologies; iii) the association between altered signalling on liver ER and the onset of metabolicdisorders; iv) the molecular interactions between ER and PPAR activity and the effect of estrogens onliver autophagy. WAYS research is facilitated by a series of tools such as ER conditional KO, reportermice, arrays of genes known as target of liver ERa, and others generated by our laboratory incollaboration with EU groups in previous EU programs. The vision of the liver as a functional unit withreproductive organs constitutes a paradigm shift in our understanding of woman physiology; thus, thefull comprehension of liver ERa activity and regulation will be a critical step for the conception of newtherapies for several diseases affecting women including the metabolic syndrome or the non-alcoholicsteatosis.

End Date:31/3/2018

mailto:[email protected]://www.unimi.it/http://www.unimi.it/mailto:[email protected]


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336204 ISLETMESENCHYME Pathophysiology and Endocrinology

Principal Investigator: Dr. Limor Landsman [email protected]

Host Institution: TEL AVIV UNIVERSITY, TEL AVIV, ILhttp://www.tau.ac.il/

ß-cell Dysfunction in Diabetes: Elucidating the Role of Islet-Associated Mesenchymal Cells

Glucose homeostasis relies on tightly controlled release of insulin by pancreatic beta-cells. Diabetes,characterized by increased blood glucose levels, is a chronic disease now reaching epidemicproportions. The most common form of this disease is Type 2 diabetes (T2D), which was previously

regarded as a disease of insulin resistance. However, work over the past decade had shifted thisparadigm by implicating beta-cell failure as a key factor in this disease. Despite major progress, thecellular and molecular basis of this T2D is far from being elucidated. Here, I present a novel pancreaticcell population, islet-associated mesenchymal cells (isMCs), which are with close contact to beta-cellsin both human and mouse pancreata. My preliminary findings revealed that isMCs function to maintainbeta-cells maturity and functionality. I therefore hypothesize that impaired isMCs function serve as anunderlying cause for diabetes. To test this hypothesis, we will characterize the continuous requirementof isMCs for glucose homeostasis by their specific depletion in vivo. Next, we will link genes associatedwith T2D to isMCs function, by manipulating their expression and elucidating the effect on beta-cellfunction. Finally, we will investigate the source of diabetes prevalence found in pancreatic cancer and

pancreatitis patients, by identifying how isMCs ability to maintain beta-cell function is affected in thesediseases. To this end, we will use transgenic mouse models and culture systems to specificallymanipulate cells and genes, and to study the resultant effect on beta-cell phenotype and glucosehomeostasis. The implications of this work are far reaching as they will point to isMCs as a new playerin glucose regulation, and as a contributor to beta-cell dysfunction in diabetes. Furthermore, thefindings of this study will implicate isMCs a novel target for therapeutic approaches to diabetes, acurrently unmet medical need.

End Date:

30/9/2018

mailto:[email protected]://www.tau.ac.il/http://www.tau.ac.il/mailto:[email protected]


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614847 LIFEWITHOUTINSULIN Pathophysiology and Endocrinology

Principal Investigator: Prof. Roberto Coppari [email protected]

Host Institution: UNIVERSITE DE GENEVE, GENEVE, CHwww.unige.ch

Metabolic actions of brain leptin receptors signaling in type 1 diabetes

An established dogma is that insulin is absolutely required for survival. This notion has been supportedby the fact that the sole life-saving intervention available to the millions affected by type 1 diabetesmellitus (T1DM; an illness caused by pancreatic β-cell loss and hence insulin deficiency) is insulin

therapy. This treatment however does not restore normal metabolic homeostasis. In fact, the life-expectancy and -quality of T1DM people is worse compared to normal subjects. In part, this is due tochallenging morbidities of T1DM, as for example heart disease and hypoglycemia, both of which arethought to be caused by insulin therapy itself. Indeed, owing to insulin ’s lipogenic actions, thistreatment likely contributes to the ectopic lipid deposition (i.e.: in non-adipose tissues) and extremelyhigh incidence of coronary artery disease seen in T1DM subjects. Also, due to insulin’s potent, fast-acting, glycemia-lowering action, this therapy significantly increases the risk of hypoglycemia; adisabling and life threatening event. Because insulin therapy does not restore metabolic homeostasis inT1DM subjects, better intervention is urgently needed. To these ends, we and others have shown thatthe hyperglycemic and lethal consequences of insulin deficiency can be rescued by administration of

the adipocyte-secreted hormone leptin. Not only these results challenge an established view, they alsoraise a fundamental biological and medical question: what are the mechanisms by which leptinimproves hyperglycemia and permits survival in the context of insulin deficiency? This proposal aims atidentifying the critical cellular and molecular components underlying the beneficial effects of leptin inthe context of insulin deficiency. Once identified, manipulation of these components has the potentialto improve life-expectancy and -quality of the millions affected by insulin deficiency (e.g.: T1DM andalso some late-stage type 2 diabetics).

End Date:

31/5/2019

mailto:[email protected]://www.unige.ch/http://www.unige.ch/mailto:[email protected]


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616917

Principal Investigator: Dr. Mario Pende

RARITOR Pathophysiology and Endocrinology

Host Institution:

[email protected] NATIONAL DE LA SANTE ET DE LA RECHERCHE MEDICALE (INSERM)PARIS, FRwww.inserm.fr

mTOR pathophysiology in rare human diseases

The mammalian Target Of Rapamycin (mTOR) is a master regulator of growth. mTOR is a protein kinasethat exists in two distinct complexes in the cell and transduces virtually all anabolic signals from the

environment: nutrients, such as glucose and amino acids, growth factor peptides, such as insulin andinsulin like growth factors, oxygen, mitochondrial metabolites, energy status. mTOR is required tosustain cell responses to nutrient availability including cell growth, proliferation, macromoleculebiosynthesis, and suppress autophagy. During the past ten years we have generated and characterizeda wide panel of mouse mutants in the mTOR pathway. We were involved in revealing specificphenotypes that increased our knowledge of mTOR roles in pathophysiology: mutants with small cells,mutants resistant to tumorigenesis in specific tissues and after specific oncogenic insults, mutantsmimicking caloric restriction and promoting longevity, mutants with muscle dystrophy, mutants withaltered insulin action. The overall goal of our research proposal for the next five years is twofold. Fromone hand we want to better understand fundamental processes including cell size control and

organismal longevity. To this end we want to determine the molecular targets of the mTORC1/S6kinase cassette that may explain the alterations in cell size and lifespan when these kinases arederegulated (project 1). From the other hand we want to understand and cure rare human geneticdiseases that arise from pathological changes in the activity of the mTOR pathway in children or thatmay benefit from therapeutical intervention on this pathway. These diseases include TuberousSclerosis Complex, PEComas and hemangiomas (project 2), metabolic diseases (projects 3), lysosomalstorage diseases (project 4). The translational approaches in this proposal will stem from a closeinteraction with multiple Medical Dept. in our shared research campus of the Necker Children Hospital.

End Date:31/1/2020

mailto:[email protected]://www.inserm.fr/http://www.inserm.fr/mailto:[email protected]


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617676 PHONICS Pathophysiology and Endocrinology

Principal Investigator: Dr. Edgar Rodrigues Almeida Gomes [email protected]

Host Institution: INSTITUTO DE MEDICINA MOLECULAR, LISBOA, PTwww.imm.ul.pt

Positioning the nucleus for cell migration and muscle fiber function

The cell nucleus is positioned at specific places within the cytoplasm and this position is important fordifferent cellular, developmental and physiological processes. Nuclear positioning depends onconnections between nuclear envelope proteins and the cytoskeleton. In migrating cells, we found that

the nucleus is positioned away from the front of the cell and this event is important for cell migration.We performed an RNAi screen for nuclear positioning and found new nuclear envelope proteinsinvolved in nuclear positioning. In fully developed myofibers, nuclei are specifically positioned at theperiphery of the myofiber, while during development and regeneration, as well as in multiple musclepathologies, the nucleus is centrally positioned. We found new mechanisms drive nuclear movementduring myofiber formation. We also showed that nuclear position is important for muscle function.However why nuclear positioning is important for myofiber activity remains an open question. Wenow propose to use unique systems to monitor cell migration and myofiber formation in combinationwith biochemistry, cell biology, high- and super-resolution microscopy approaches to: 1) Identify novelmolecular mechanisms that mediate nuclear positioning during cell migration and myofiber formation.

3) Determine a role for nuclear positioning in myofiber function as well as the significance of alterednuclear positioning in different forms of muscle pathology. The proposed work will establish newmechanisms for nuclear positioning. Importantly, by identifying mechanisms and understanding therole of nuclear positioning in myofiber function, we will lay the foundations for future studies toameliorate or treat muscle disorders as well as other conditions where nucleus positioning may proveto play a role such as cancer.

End Date:30/6/2019

mailto:[email protected]://www.imm.ul.pt/http://www.imm.ul.pt/mailto:[email protected]


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637458 MISTRANSMITO Pathophysiology and Endocrinology

Principal Investigator: Dr. Henna Riikka Susanna Tyynismaa [email protected]

Host Institution: HELSINGIN YLIOPISTO, HELSINKI, FIhttp://www.helsinki.fi/university/

Tissue-specific mitochondrial signaling and adaptations to mistranslation

Mitochondria play a central role in the energy metabolism of our bodies and their defects give rise to alarge variety of clinical phenotypes that can affect practically any tissue. The mechanisms for thetissue-specific outcomes of mitochondrial diseases are poorly understood. Mitochondrial energy

production relies on two separate protein synthesis machineries, cytoplasmic and mitochondrial, butthe mechanisms regulating the concerted actions between the two are largely to be discovered.Defects in either protein synthesis system that lead to accumulation of mistranslated mitochondrialproteins, intrinsic or imported from the cytoplasm, result in stress signals from mitochondria and inadaptive responses within the organelle and the entire cell. My hypothesis is that some of these signalsand adaptive mechanisms are tissue-specific. My group will test the hypothesis by 1) generating andcharacterizing mouse models of cytoplasmic and mitochondrial mistranslation to be able to addressour questions in different tissues. 2) We will develop methods for detection of ribosome stalling inmouse tissues to identify the consequences of mistranslation for individual proteins. 3) We will usesystems biology approaches to identify stress signal responses to mitochondrial and/or cytoplasmic

mistranslation using different tissues of our models, to identify those that are unique or global. 4) Ourprevious study has identified an interesting candidate responder to mistranslation stress and we willtest the role of this factor in knockout animal models and by crossing with the mistranslation mice. Iexpect to gain important new knowledge of in vivo responses to mistranslation and execution ofquality control. This proposal investigates key questions in understanding differential tissueinvolvement in metabolic defects, and will provide new directions for utilization of tissue-specificadaptations in finding interventions for mitochondrial diseases.

End Date:

30/6/2020

mailto:[email protected]://www.helsinki.fi/university/http://www.helsinki.fi/university/mailto:[email protected]


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638193 CRCStemCellDynamics Pathophysiology and Endocrinology

Principal Investigator: Dr. Louis Vermeulen [email protected] Medisch Centrum bij de Universiteit van Amsterdam,

Host Institution: AMSTERDAM, NLwww.amc.nl

Molecular Subtype Specific Stem Cell Dynamics in Developing and Established Colorectal Cancers

Annually 1.2 million new cases of colorectal cancer (CRC) are seen worldwide and over 50% of patientsdie of the disease making it a leading cause of cancer-related mortality. A crucial contributing factor to

these disappointing figures is that CRC is a heterogeneous disease and tumours differ extensively in theclinical presentation and response to therapy. Recent unsupervised classification studies highlight thatonly a proportion of this heterogeneity can be explained by the variation in commonly found (epi-)genetic aberrations. Hence the origins of CRC heterogeneity remain poorly understood. The centralhypothesis of this research project is that the cell of origin contributes to the phenotype and functionalproperties of the pre-malignant clone and the resulting malignancy. To study this concept I willgenerate cell of origin- and mutation-specific molecular profiles of oncogenic clones and relate those tohuman CRC samples. Furthermore, I will quantitatively investigate how mutations and the cell of originact in concert to determine the functional characteristics of the pre-malignant clone that ultimatelydevelops into an invasive intestinal tumour. These studies are paralleled by the investigation of stem

cell dynamics within established human CRCs by means of a novel marker independent lineage tracingstrategy in combination with mathematical analysis techniques. This will provide critical andquantitative information on the relevance of the cancer stem cell concept in CRC and on the degree ofinter-tumour variation with respect to the frequency and functional features of stem-like cells withinindividual CRCs and molecular subtypes of the disease. I am convinced that a better and quantitativeunderstanding of the dynamical properties of stem cells during tumour development and withinestablished CRCs will be pivotal for an improved classification, prevention and treatment of CRC.

End Date:

31/3/2020

mailto:[email protected]://www.amc.nl/http://www.amc.nl/mailto:[email protected]


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638891 NutrientSensingVivo Pathophysiology and Endocrinology

Principal Investigator: Dr. Alejo Efeyan [email protected] CENTRO NACIONAL DE INVESTIGACIONES ONCOLOGICAS

Host Institution: CARLOS III, MADRID, ESwww.cnio.es

The Physiology of Nutrient Sensing by mTOR

A major role of metabolic alterations in the development of several human diseases, as diabetes,cancer and in the onset of ageing is becoming increasingly evident. This has a deep impact for human

health due to the alarming increase in nutrient intake and obesity in the last decades. Fundamentalaspects of how aberrant nutrient fluctuations trigger deregulated hormone levels and endocrinesignals have been elucidated, being a prime example the phenomenon of insulin resistance. Incontrast, how changes in nutrient levels elicit direct cell-autonomous signal transduction cascades andthe consequences of these responses in physiology are less clear.The signalling circuitry of directnutrient sensing converges with that of hormones in the regulation of the mechanistic target ofrapamycin (mTOR) kinase, a driver of anabolism, cell growth and proliferation. Deregulation ofmTORC1 activity underlies the pathogenesis of cancer and diabetes, and its inhibitor rapamycin isapproved as an anti-cancer agent and delays ageing from yeast to mammals. In spite of its importancefor human disease, our understanding of the nutrient sensing signalling pathway and its impact in

physiology is largely incomplete, as only a few years ago the direct molecular link between nutrientsand mTORC1 activation, the Rag GTPases, were identified.The present proposal aims to determine howthe nutrient sensing signalling pathway affects mammalian physiology and metabolism, and whetherits deregulation contributes to cancer, insulin resistance and aging. In particular, the objectives are: 1)To identify novel regulators of the Rag GTPases with unbiased and candidate-based approaches. 2) Toestablish the consequences of deregulated nutrient-dependent activation of mTORC1 in physiology, bymeans of genetically engineered mice. 3) To determine the impact of the nutrient sensing pathway inthe effects of dietary restriction and nutrient limitation in glucose homeostasis and cancer.

End Date:31/12/2020

mailto:[email protected]://www.cnio.es/http://www.cnio.es/mailto:[email protected]


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639382 aCROBAT Pathophysiology and Endocrinology

Principal Investigator: Prof. Zachary Philip Gerhart-Hines [email protected]

Host Institution: KOBENHAVNS UNIVERSITET, COPENHAGEN N, DKwww.ku.dk

Circadian Regulation Of Brown Adipose Thermogenesis

Obesity and diabetes have reached pandemic proportions and new therapeutic strategies are criticallyneeded. Brown adipose tissue (BAT), a major source of heat production, possesses significant energy-dissipating capacity and therefore represents a promising target to use in combating these diseases.

Recently, I discovered a novel link between circadian rhythm and thermogenic stress in the control ofthe conserved, calorie-burning functions of BAT. Circadian and thermogenic signaling to BATincorporates blood-borne hormonal and nutrient cues with direct neuronal input. Yet how theseresponses coordinately shape BAT energy-expending potential through the regulation of cell surfacereceptors, metabolic enzymes, and transcriptional effectors is still not understood. My primary goal isto investigate this previously unappreciated network of crosstalk that allows mammals to effectivelyorchestrate daily rhythms in BAT metabolism, while maintaining their ability to adapt to abruptchanges in energy demand. My group will address this question using gain and loss-of-function in vitroand in vivo studies, newly-generated mouse models, customized physiological phenotyping, andcutting-edge advances in next generation RNA sequencing and mass spectrometry. Preliminary, small-

scale validations of our methodologies have already yielded a number of novel candidates that maydrive key facets of BAT metabolism. Additionally, we will extend our circadian and thermogenic studiesinto humans to evaluate the translational potential. Our results will advance the fundamentalunderstanding of how daily oscillations in bioenergetic networks establish a framework for theanticipation of and adaptation to environmental challenges. Importantly, we expect that thesemechanistic insights will reveal pharmacological targets through which we can unlock evolutionaryconstraints and harness the energy-expending potential of BAT for the prevention and treatment ofobesity and diabetes.

End Date:30/4/2020

mailto:[email protected]://www.ku.dk/http://www.ku.dk/mailto:[email protected]


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646849 LYMPHORG Pathophysiology and Endocrinology

Principal Investigator: Dr. Taija Marianna Makinen [email protected]

Host Institution: UPPSALA UNIVERSITET, UPPSALA, SEwww.uu.se

Organ-specific mechanisms of lymphatic vascular development and specialisation

Lymphatic vasculature maintains tissue fluid homeostasis and has important emerging roles ininflammation, immunity, lipid metabolism, blood pressure regulation and cancer metastasis. Lymphaticvessels are specialised to fulfil the functional needs of different organs while diseases associated with

lymphatic dysfunction frequently affect vessels of specific tissues. How functional specialisation ofvessels is achieved and what underlies tissue-specific vessel failure is not understood. I hypothesisethat organ-specific manifestation of lymphatic dysfunction in disease is due to vascular bed-specificdifferences in vessel formation. In this project my aim is to identify genes and mechanisms required fororgan-specific lymphatic development. Building on our recent discovery of a previously unknownprogenitor cell type that is required for lymphatic development in an organ-specific manner I set out toidentify the origin and function of lymphatic endothelial progenitor cells (LEPC) during developmentand assess their potential for therapeutic lymphatic regeneration. Towards this aim, we will identifyorgan-specific origins of lymphatic vasculature using lineage tracing and determine genetic signaturesof lymphatic endothelial progenitors by mRNA sequencing. Cells and tissues from normal and mutant

mice that show organ-specific lymphatic defects will be analysed. To identify molecular and cellularmechanisms of LEPC derived vessel formation, we will functionally characterise LEPC signature genesusing mouse models and visualise vessel development by in vivo two-photon microscopy. The functionand therapeutic potential of LEPCs and LEPC derived vessels will be assessed using mouse models oftolerance, inflammation, obesity and lymphoedema. This work will provide novel insights into organ-specific mechanisms of vascular morphogenesis and identify a progenitor cell that may be expoited torestore lymphatic function in disorders associated with lymphatic vessel failure.

End Date:

30/4/2020

mailto:[email protected]://www.uu.se/http://www.uu.se/mailto:[email protected]


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646903 INFANTLEUKEMIA Pathophysiology and Endocrinology

Principal Investigator: Prof. Pablo Menéndez Buján [email protected]ó Institut de Recerca Contra la Leucemia Josep Carreras, BARCELONA,

Host Institution: ESwww.carrerasresearch.org

GENOMIC, CELLULAR AND DEVELOPMENTAL RECONSTRUCTION OFINFANT MLL-AF4+ ACUTE LYMPHOBLASTIC LEUKEMIA

Infant cancer is very distinct to adult cancer and it is progressively seen as a developmental disease. An

intriguing infant cancer is the t(4;11) acute lymphoblastic leukemia (ALL) characterized by the hallmarkrearrangement MLL-AF4 (MA4), and associated with dismal prognosis. The 100% concordance in twinsand its prenatal onset suggest an extremely rapid disease progression. Many key issues remain elusive:Is MA4 leukemogenic? Which are other relevant oncogenic drivers? Which is the nature of the celltransformed by MA4? Which is the leukemia-initiating cell (LIC)? Does this ALL follow a hierarchical orstochastic cancer model? How to explain therapy resistance and CNS involvement? To what extent dogenetics vs epigenetics contribute this ALL?These questions remain a challenge due to: 1) the absenceof prospective studies on diagnostic/remission-matched samples, 2) the lack of models which faithfullyreproduce the disease and 3) a surprising genomic stability of this ALL.I hypothesize that a Multilayer-Omics to function appro

2015-11 list of erc nrf sa.pdf

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