PDF file: EURASNET Annual Report 2008

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Participant 21 – Angela Krämera) Work performed during the period• WP2Provided EURASNET members with antibodies and plasmids• WP8– Optimization of CLIP of SF1 and U2AF65 for high-throughput sequencing– Analysis of SF1 in AS of UPF3a pre-mRNA (identified as a SF1 target by CLIP)• WP11– Cataloguing SF1 isoforms in HeLa cells and mouse tissues by Western blottingantibodies against different SF1 epitopes– Generation of antibodies against additional SF1 isoforms (Dundee Cell Products)– Identification of immunoprecipitated SF1 isoforms and SF1 interacting proteinsby mass spectrometry (in collaboration with Henning Urlaub)• WP16– Co-organiser of the “First International EURASNET Conference on AlternativeSplicing” in Krakow, May 21-23, 2008– Attendance of EURASNET conferences, workshops and IFMs as detailed below(see “Travel”)• WP17Coordination of staff exchange and training• WP21Co-organizer (together with Daniel Schümperli and Oliver Mühlemann) of theAnnual Swiss RNA Workshop in Bern, to be held on January 30, 2009. Thisworkshop is sponsored by the Swiss Committee for Molecular Biology (funded bythe Swiss National Science Foundation), with ca. 120 participants, 14 short talksselected from submitted abstracts, 2 talks from invited speakers (Benoit Chabot andMatthias Hentze) and poster sessions.• WP22Participation in telephone conferences and discussions of management membersb) Major cost items with justificationParticipant 1A Type of expenditure Budget total costspersonnel 8,647.07consumables 684.70trainingequipmenttravel 1,344.84= total direct costs 10,676.61+ overhead 2,135.32= total eligible costs 12,811.93Major cost items177
• ResearchPersonnelIvona Bagdiul [WP 8] 475 hr 8,647.07 EuroConsumablesChemicalsLaboratory suppliesOthersTravel520.42 Euro195.78 Euro-31.50 Euro1,344.84 Euro– EURASNET meeting, Berlin, Germany (Angela Krämer)– EURASNET Workshop - Alternative Splicing and Disease, Montpellier, France(Nicolas Antih)– First International EURASNET Conference on Alternative Splicing, Krakow,Poland (Angela Krämer, Ivona Bagdiul)– EURASNET annual reporting meeting 2008, Krakow, Poland (Angela Krämer)– EURASNET Workshop - Interdisciplinary Focus Meeting on BiophysicalMethods Applied to RNA, Aarhus, Denmark (Maria Choleza)• Dissemination– First International EURASNET Conference on Alternative Splicing, Krakow,Poland (Poster)– 33rd FEBS Conference/11th IUBMB Congress: Biochemistry of CellRegulation, Athens, Greece (invited talk)– 13th Annual Meeting of the RNA Society, Berlin, Germany (Poster)178
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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
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Work Package 6 In silico approaches
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alternative splicing.162 Compare sp
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33 Agreement on pre-mRNA substrates
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its numerous binding sites on both
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Work Package 8 Genome-wide Analyses
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173 Further development of data ana
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Problems and explanations for delay
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eveal that there is a dramatic chan
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Work Package 10 Post-translational
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mutational analysis that led to the
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Isolation of an active step I splic
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FBP11 and 21 with these sequences.
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Similarly to what observed for SF2/
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prp45-113 mutant, which is compatib
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cell lines. In contrast in the pres
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genes with roles in the development
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Structural analyses of several RRMs
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Work Package 17 Staff Exchange and
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Barralle's lab, Krämer is acting a
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alternative splicing) and higher ed
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Student Symposium “Decision Makin
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variation and suitability for use w
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Following feedback from members we
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Invited seminars: In addition to me
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Publications 2008Author Title Publi
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Author Title Publication EURASNET P
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Minutes of the General Assembly dec
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241 Evaluate available careerdevelo
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156 The EURASNET memberStamm publis
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y coarse-grained foldingsimulation.
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overexpressor and mutant lines(mont
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machinery with particularrespect to
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alternative splicing, using theEDI
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contemporary findings withinthe EUR
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Licht K, Medenbach J, Lührmann R,K
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9 TABULAR OVERVIEW OF MAJOR COST IT
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total costs * 18.891,12 52778.60 41
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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
Page 132 and 133: Participant 1B - Karla Neugebauera)
Page 134 and 135: Participant 2 - Juan Valcarcela) Wo
Page 136 and 137: Participant 3 - Stefan Stamma) Work
Page 138 and 139: Participant 4 - Göran Akusjärvia)
Page 140 and 141: Participant 5A/B - Peer Bork/Rolf A
Page 142 and 143: Major cost items• ResearchPersonn
Page 144 and 145: Participant 7 - Francisco Barallea)
Page 146 and 147: Francisco Baralle gave a talk to a
Page 148 and 149: alternative splicing on human disea
Page 150 and 151: J. Beggs has had frequent contact w
Page 156 and 157: Participant 12A - Jamal Tazia) Work
Page 158 and 159: Participant 12B - Bertrand Séraphi
Page 160 and 161: Participant 12C - Christiane Branla
Page 162 and 163: Participant 12D - Edouard Bertranda
Page 164 and 165: Participant 13 - Daniel Schümperli
Page 166 and 167: Participant 14 - John W. S. Browna)
Page 168 and 169: Participant 15 - Javier F. Cáceres
Page 170 and 171: • ResearchPersonnelName WP Person
Page 172 and 173: MiscellaneousOligonucleotidesUse of
Page 174 and 175: Major cost items• ResearchConsuma
Page 180 and 181: Participant 22 - Angus Lamonda) Wor
Page 182 and 183: Participant 23 - Chris Smitha) Work
Page 184 and 185: ChemicalsEnzymesLaboratory supplies
Page 186 and 187: Participant 26 - Didier Auboeufa) W
Page 188 and 189: tool for the molecular analysis of
Page 190 and 191: Participant 29 - Frédéric Allaina
Page 192 and 193: protein and instead possesses the d
Page 194 and 195: + overhead 4.730= total eligible co
Page 196 and 197: Claudia Tamaro (PhD) has begun work
Page 198 and 199: ETHZIIMCBUPFSOTON-HGDTOTALJoint Pro
Page 200 and 201: Direct eligible costs 53.240,48 0,0
Page 202 and 203: Direct eligible costs 18.720,07 0,0
Page 204 and 205: 13 REPORT ON THE DISTRIBUTION OF TH
Page 206 and 207: Report on the Distribution of the C
Page 208 and 209: For most work packages here follows
Page 210 and 211: pathways (eg, Reactome ).While PAND
Page 212 and 213: The possible dependence of the effe
Page 214 and 215: In some treatments or mutants, simi
Page 216 and 217: Work Package 12: Mis-splicing and D
Page 218 and 219: acid. Furthermore, using antibodies
Page 220 and 221: At the 2007 annual meeting in Ile d
Page 222 and 223: Partner 13 has extensively studied
Page 224 and 225: inhibitors/modulators of RNA splici
Page 226 and 227: 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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