PDF file: EURASNET Annual Report 2008

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+ overhead 4.730= total eligible costs 28.380Major cost itemsResearch1. Personnel1.A 3 rd cycle grant for Eneritz Aguirre (WP13) 10 PM (= 1.3667 hours) 12.829,10 Euro1.B Part-time grant for Juán-Ramón Gonzàlez-Vallinas (WP8) 2 PM (= 137 hours) 1.200 Euro2. Other2.A Registration of E. Aguirre to the Annual Meeting of the Society of Molecular Biology and Evolution (SMBE). Barcelona.5/06/08 - 8/06/2008 (370 eur)2.B Registration André Corvelo and Mireia Plass to the 1 st EURASNET conference (702,70 eur)2.C Registration Eduardo Eyras and Eneritz Aguirre to the 1 st EURASNET conference (705,40 eur)2.D Publication cost of article by E. Eyras in Journal Genome Biology. (Corvelo et al. Genom Biol 2008) (1.756,89 Eur)2.E Registration and Hotel of E. Eyras' group to the IFM EURASNET Meeting on High Throughput Technologies and Splicing,Valencia, Feb/2009. (1.242,99 eur)3. Equipment CS1Invoice DateCostdepreciation ofequipment3.A Computer for Eneritz Aguirre(HP xw9400 Workstation + Hp Linux Installer Kit+Monitor HPLP2065) 02-abr-08 3.660,00 813,333.B Back-up system for Eduardo Eyras' group 20-nov-08 289,00 11,243.C Back-up Software for Eduardo Eyras' group 16-dic-08 228,90 2,993.D Renewal website (www.alternative-splicing.org) Eduardo Eyrasfor the IFM EURASNET meeting on alternative splicing, Stockholm,June 2009 16-dic-08 82,80 1,084. Travel costs4.260,70 828,64DESCRIPTIONCOST4.A Meeting of PIs of EURASNET network at Berlín (Eduardo Eyras) 20-23 January 2008 37,004.B Barcelona-Krakow plane tickets (E.Eyras, E.Aguirre, M. Plass & A. Corvelo) 21/05/08 - 25/05/08 1.882,524.C Mireya Plass – Travel expenses Krakow meeting 21/05/08-23/05/08 179,934.D Eduardo Eyras – Travel expenses Krakow meeting 21/05/08 - 25/05/08 109,214.E Eneritz Aguiirre – Travel expenses Krakow meeting 21/05/08-23/05/08 23,254.F Invitation to Scott Roy. Research visit and seminar at Eyras' Lab 19/05/08 122,004.G Research visit of Mariano Allo (A. Kornblihtt's lab) to Eyras' Lab 1/06/08 - 15/06/08 Barcelona 985,844.H Eduardo Eyras. Workshop Alternative Splicing in animals and Plants 3/10/2008, Milan, Italy. InvitedSeminar 159,034.I Research visit of Eduardo Eyras to F. Allain's lab (Zurich) (Invited seminar and member of thesiscommittee) 322,874.J André Corvelo – AS-SIG 2008 meeting in Toronto, ISMB2008 192,63193
Participant 32 – Diana Barallea) Work performed during the periodWP2: SHARING RESOURCES, TECHNOLOGY AND RELIABLEPROTOCOLSFurther refinement of the minigene system for routine use in diagnosticlaboratories is in progress. As described in the WP12 report at deliverable214, the minigene system has been supplied to several researchers in otherresearch institutions. In addition I am writing an invited EMBOreportsViewpoint for publication in 2009.WP12: MIS-SPLICING AND DISEASEWe have studied several regulatory elements in genes of interest(NF-1, BRCA, and Nde). In particular with regards to, RNA-protein andRNA-RNA interactions. Two successful projects that have led topublications this year in the NF1 gene have included the identification of thefactor PTB as a negative regulator for pseudoexons and showing that there islow U1 snRNP dependence at the NF1 exon 29 donor splice site. Ongoingwork includes: Study of BRCA 1 gene exon 11 where purifying selectionacts in the BRCA1 conserved region spanning exon 9, exon 10 and exon 11preventing aberrant splicing and analysing the splicing regulatory systemsinvolved. Also, we are looking at the splicing evolution of the Nde geneknown to be involved in cortical growth and if dysfunctional will causemicrocephaly.• WP16: CONFERENCES AND MEETINGSPID32 has reported on the organization of a workshop in London (3 March2008) to discuss RNA Splicing and Diagnostics with the heads of moleculardiagnostic labs. in the UK– see meeting report.PID32 will organize a 2 nd workshop in Paris on 1 st October 2009 again withdiagnostic laboratories particularly in France but with open invitation toEurope, to come to a consensus agreement and develop guidelines for RNAand splicing analysis in clinical practice.• WP17: STAFF EXCHANGE AND TRAININGOur new PhD student (Claudia Tamaro) has had pre fellowship training atthe laboratory of Prof Baralle in Trieste, after which she moved to ourlaboratory in October 2008. We have collaborated with the ICGEB and theUniversity of Cambridge- Smith lab. on various projects, involving visits tothe labs. In partiuclar my post doc. M. Raponi learnt RNAi for PTB at theSmith lab. in the winter of 2008, and has had collaborative and teachingmeetings at Trieste. This included learning about UV crosslinking and pulldown analysis for the purposes of setting this up in our own lab. The Smithcollaboration resulted in a joint publication.• WP18: CAREER DEVELOPMENTMichela Raponi (post doc) has attended and presented at the RNA UKmeeting Jan 08 and the Montpellier practical workshop Feb. 08. She has alsopresented her work at the University of Southampton postgraduateconference this year. She has attended 2 professional courses at theUniversity: ‘How to write grants’ and a microscopy course.194
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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
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travel 6.964,91overhead 3.081,07oth
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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
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 152 and 153: Major cost items• ResearchPersonn
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 178 and 179: Participant 21 - Angela Krämera) W
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 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
Page 228 and 229: 15.3 GRAPHICAL PRESENTATION OF WORK
Page 230 and 231: 15.4 TABLE OF MILESTONES (MONTH 37-
Page 232 and 233: 156 The EURASNET memberStamm publis
Page 234 and 235: 194 Bertrand will analyze indetail
Page 236 and 237: 216 Aubeouf and Neugebauer willcoll
Page 238 and 239: 238 Establishing joint PhDcommittee
Page 240 and 241: 283 A unified browser for allknown
Page 242 and 243: 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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