PDF file: EURASNET Annual Report 2008

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Author Title Publication EURASNET Public. +/- 1 EURASNETacknowledgement 2Glockshuber R., Kuennemann E. Forest virus capsid protein. Biology 376, 721-35.Auweter S.D., Allain F.H.-T.Lapouge, K., Schubert, M,. Allain, F.H.-T.,Haas, D.Structure-function relationships of the polypyrimidinetract binding protein.Gac/Rsm signal transduction pathway of gammaproteobacteria:from RNA recognition to regulation ofsocial behaviour.Cellular and Molecular LifeSciences 65, 516-27.Kim, E., Goren, A. and Ast, G. Alternative splicing and disease. RNA Biology 2008 Mar22;5(1). [epub ahead ofprint]Ram, O., Schwartz, S. and Ast. G.Gal-Mark, N., Schwartz, S. and Ast, G.Goren, A., Kim, E., Amit, M., Bochner, R.,Lev-Maor, G., Ahituv, N. and Ast, G.Multifactorial interplay controls the splicing profile ofAlu derived exons.Alternative splicing of Alu exons--two arms are betterthan one.Alternative approach to a heavy weight problem.- -Molecular Microbiology 67,241-253. - -Molecular and CellularBiology 2008 Mar 10. [epubahead of print]Nucleic Acids Research2008 Feb 14.Genome Research 2008 Feb.- +- -- -- +Kim, E., Goren, A. and Ast, G. Alternative splicing: current perspectives. Bioessays 30(1), 38-47. - -Kim, E., Goren, A. and Ast, G..Sanchez, G., Bittencourt, D., Laud, K.,Barbier, J., Delattre, O., Auboeuf, D.,Dutertre, M.Simpson, C.G., Fuller, J., Maronova, M.,Kalyna, M., Davidson, D., McNicol, J.,,Barta, A., and Brown , J.W.S.de la Fuente van Bentem, S., Anrather, D.,Dohnal, I., Roitinger, E., Csaszar, E.,Joore, J., Buijnink, J., Carreri, A., Forzani,C., Lorkovic, Z.J., Barta, A., Lecourieux,D., Verhounig, A., Jonak, C., and Hirt, H.Insights into the connection between cancer andalternative splicing.Alteration of cyclin D1 transcript elongation by amutated transcription factor up-regulates the oncogenicD1b splice isoform in cancer.Monitoring changes in alternative precursor messengerRNA splicing in multiple gene transcriptsSite-Specific Phosphorylation Profiling of ArabidopsisProteins by Mass Spectrometry and Peptide ChipAnalysis.Trends in Genetics 2008Jan.Proceedings of the NationalAcademy of Sciences USA2008 Apr 14. [epub ahead ofprint]- +- +The Plant Journal 53, 1035–1048. + +Journal of ProteomeResearch 2008 Apr 24.[epub ahead of print] - -81
Author Title Publication EURASNET Public. +/- 1 EURASNETacknowledgement 2Simpson, C.G., Lewandowska, D., Fuller,J., Maronova, M., Kalyna, M., Davidson,D.,McNicol, J.,, Raczynska, D.,Jarmolowski, A., Barta, A., and Brown,J.W.S.Lorkovic, Z.J., Hilscher, J. and Barta, A.Raponi, M., Baralle, D.Romano, M., Bacalini, M.G., Verschoor,E.J., Crovella, S., Baralle, F.E.Ayala, Y.M., Misteli, T., Baralle, F.E.Buratti, E., Baralle, F.E.Alternative Splicing in PlantsCo-localisation studies of Arabidopsis SR splicingfactors reveal different types of speckles in plant cellnuclei.Can donor splice site recognition occur without theinvolvement of U1 snRNP?Origin and evolution of the c.844_845ins68/c.833T>Cmutations within the cystathionine beta-synthase genein great apes.TDP-43 regulates retinoblastoma proteinphosphorylation through the repression of cyclindependentkinase 6 expression.Multiple roles of TDP-43 in gene expression, splicingregulation, and human disease.Biochemical SocietyTransactions. (accepted)+ +Experimental Cell Research.(accepted) - +Biochemical SocietyTransactions 36(3).FEBS Letters 582(3), 423-426. - +Proceedings of the NationalAcademy of Sciences USA105(10), 3785-3789.Frontiers in Bioscience 13,867-878.Simpson, C.G. and Brown, J.W.S. Plant U12-dependent (AT-AC) introns. In: Nuclear pre-mRNAprocessing in plants. Ed.Reddy, A.S.N. (in press)Brown, J.W.S. and Shaw, P.J. The plant nucleolus and mRNA biogenesis. In: Nuclear pre-mRNAprocessing in plants. Ed.Reddy, A.S.N. (in press)Schwartz, S.H., Silva, J., Burstein, D.,Pupko, T., Eyras, E., Ast, G.Ellis, J.D., Lleres, D., Denegri, M.,Lamond, A.I. and Caceres, J.F.Matic, I., van Hagen, M., Schimmel, J.,Macek, B., Ogg, S. C., Tatham, M. H.,Hay, R. T., Lamond, A. I., Mann, M. andVertegaal, A. C.Large-scale comparative analysis of splicing signals andtheir corresponding splicing factors in eukaryotes.Spatial mapping of splicing factor complexes involvedin exon and intron definition.In vivo identification of human small ubiquitin-likemodifier polymerization sites by high accuracy massspectrometry and an in vitro to in vivo strategy.Genome Research 18(1), 88-103.Journal of Cell Biology181(6), 921-34.Molecular and CellularProteomics 7, 132-44.- +- -- -- -+ +Le Hir, H. and Séraphin, B. EJCs at the heart of translational control. Cell 133(2), 213-6. - -82
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TABLE OF CONTENTSA. PERIODIC ACTIVI
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1 PUBLISHABLE EXECUTIVE SUMMARY EUR
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Dr. Davide Gabellini(28) Swiss Inst
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WP7 Molecular characterization of s
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To identify protein-protein interac
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expressed in a particular tissue. T
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Duchenne muscular dystrophy (DMD).
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WP21 Reachout to the broader RNA co
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4.1 TABLE OF MILESTONES JPA MONTH 2
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Numerous plasmids, constructs, extr
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collaboration between EURASNET and
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5.1 WORK PACKAGE REPORTSWork Packag
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• Ongoing regular addition of new
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Work Package 4 The Alternative Spli
Page 31 and 32: Work Package 6 In silico approaches
Page 33 and 34: alternative splicing.162 Compare sp
Page 35 and 36: 33 Agreement on pre-mRNA substrates
Page 37 and 38: its numerous binding sites on both
Page 39 and 40: Work Package 8 Genome-wide Analyses
Page 41 and 42: 173 Further development of data ana
Page 43 and 44: Problems and explanations for delay
Page 45 and 46: eveal that there is a dramatic chan
Page 47 and 48: Work Package 10 Post-translational
Page 49 and 50: mutational analysis that led to the
Page 51 and 52: Isolation of an active step I splic
Page 53 and 54: FBP11 and 21 with these sequences.
Page 55 and 56: Similarly to what observed for SF2/
Page 57 and 58: prp45-113 mutant, which is compatib
Page 59 and 60: cell lines. In contrast in the pres
Page 61 and 62: genes with roles in the development
Page 63 and 64: Structural analyses of several RRMs
Page 65: Work Package 17 Staff Exchange and
Page 69 and 70: Barralle's lab, Krämer is acting a
Page 71 and 72: alternative splicing) and higher ed
Page 73 and 74: Student Symposium “Decision Makin
Page 75 and 76: variation and suitability for use w
Page 77 and 78: Following feedback from members we
Page 79 and 80: Invited seminars: In addition to me
Page 81: Publications 2008Author Title Publi
Page 85 and 86: Author Title Publication EURASNET P
Page 93 and 94: Minutes of the General Assembly dec
Page 96 and 97: 241 Evaluate available careerdevelo
Page 98 and 99: 156 The EURASNET memberStamm publis
Page 100 and 101: y coarse-grained foldingsimulation.
Page 102 and 103: overexpressor and mutant lines(mont
Page 104 and 105: machinery with particularrespect to
Page 106 and 107: alternative splicing, using theEDI
Page 108 and 109: contemporary findings withinthe EUR
Page 118 and 119: Licht K, Medenbach J, Lührmann R,K
Page 122 and 123: 9 TABULAR OVERVIEW OF MAJOR COST IT
Page 124 and 125: total costs * 18.891,12 52778.60 41
Page 126 and 127: other (the rest) 48,57 0 56.539,43t
Page 128 and 129: travel 6.964,91overhead 3.081,07oth
Page 130 and 131: Participant 1A Type of expenditure
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Participant 1B - Karla Neugebauera)
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Participant 2 - Juan Valcarcela) Wo
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Participant 3 - Stefan Stamma) Work
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Participant 4 - Göran Akusjärvia)
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Participant 5A/B - Peer Bork/Rolf A
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Major cost items• ResearchPersonn
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Participant 7 - Francisco Barallea)
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Francisco Baralle gave a talk to a
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alternative splicing on human disea
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J. Beggs has had frequent contact w
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Page 154 and 155:
Page 156 and 157:
Participant 12A - Jamal Tazia) Work
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Participant 12B - Bertrand Séraphi
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Participant 12C - Christiane Branla
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Participant 12D - Edouard Bertranda
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Participant 13 - Daniel Schümperli
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Participant 14 - John W. S. Browna)
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Participant 15 - Javier F. Cáceres
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• ResearchPersonnelName WP Person
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MiscellaneousOligonucleotidesUse of
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Major cost items• ResearchConsuma
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Page 178 and 179:
Participant 21 - Angela Krämera) W
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Participant 22 - Angus Lamonda) Wor
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Participant 23 - Chris Smitha) Work
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ChemicalsEnzymesLaboratory supplies
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Participant 26 - Didier Auboeufa) W
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tool for the molecular analysis of
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Participant 29 - Frédéric Allaina
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protein and instead possesses the d
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+ overhead 4.730= total eligible co
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Claudia Tamaro (PhD) has begun work
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ETHZIIMCBUPFSOTON-HGDTOTALJoint Pro
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Direct eligible costs 53.240,48 0,0
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Direct eligible costs 18.720,07 0,0
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13 REPORT ON THE DISTRIBUTION OF TH
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Report on the Distribution of the C
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For most work packages here follows
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pathways (eg, Reactome ).While PAND
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The possible dependence of the effe
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In some treatments or mutants, simi
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Work Package 12: Mis-splicing and D
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acid. Furthermore, using antibodies
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At the 2007 annual meeting in Ile d
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Partner 13 has extensively studied
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inhibitors/modulators of RNA splici
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18 MONTH JPA: WORKPACKAGE TIMECOURS
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15.3 GRAPHICAL PRESENTATION OF WORK
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15.4 TABLE OF MILESTONES (MONTH 37-
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156 The EURASNET memberStamm publis
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194 Bertrand will analyze indetail
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216 Aubeouf and Neugebauer willcoll
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238 Establishing joint PhDcommittee
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283 A unified browser for allknown
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296 Group 12a (Branlant) willuse th
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315 Lamond will use a FLIM-FRET bas
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329 GROUP 7 (F. BARALLE)will contin
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333 GROUP 27 (GABELLINI)will:1) foc
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345 Schümperli’s group isplannin
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366 Quarterly network e-mail atmont
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2. Sharing Resources, Technology an
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5. Ensuring DurabilityWorkpackage d
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7. Molecular Characterization of Sp
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8. Genome-wide Analyses of Splicing
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9. Complexity of Spliceosomal Prote
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202 Srebrow will investigate the ro
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12. Mis-splicing and DiseaseWorkpac
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13. Co-transcriptional Mechanisms o
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14. Chemical Biology and Therapeuti
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15. Development of Enabling Technol
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269 IFMs in 20091. “Alternative a
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18. Career DevelopmentWorkpackage d
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20. SMEs and Technology TransferWor
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21. Reachout to the Broader RNA Com
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15.7 WORK PACKAGE LIST (MONTHS 37-5
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ETHZIIMCBUPFSOTON-HGDTOTALJoint Pro
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AMU 5 29 8 42UAAR 5 145 16 1665 29
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Joint Programme of Activities RESEA
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60 month period 18 month periodRequ
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Integration1. Young Investigator Pr
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UCAM-DBIOC 2350,000x1/3 € 50,000x
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the management team. Audit costs ar
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