PDF file: EURASNET Annual Report 2008

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Prof. Andrea Barta(9) The University of Edinburgh, Edinburgh, UKProf. Jean Beggs(10) Consiglio Nazionale delle Ricerche, Rome ItalyDr. Giuseppe Biamonti, Istituto di Genetica Molecolare - CNR, PaviaProf. Glauco Tocchini-Valentini, Istituto di Biologia Cellulare - CNR, Monterotondo Scalo (Roma)(11) Justus Liebig Universität Giessen, Giessen, GermanyProf. Albrecht Bindereif(12) Centre National de Recherche Scientifique, Paris, FranceProf. Jamal Tazi, , Institut de Genetique Moleculaire (JRU 5535 CNRS-UMII) MontpellierDr. Bertrand Séraphin, Centre de Genetique Moleculaire (CGM), UPR2167 CNRS Gif-sur-Yvette, FranceDr. Christiane Branlant, Maturation des ARN et Enzymologie Moléculaire MAEM UMR 7567 CNRS-UHP,Vandoeuvre les NancyDr. Edouard Bertrand, Institut de Genetique Moleculaire (JRU 5535 CNRS-UMII) Montpellier(13) University of Berne, Bern, SwitzerlandProf. Daniel Schümperli(14) Scottish Crop Research Institute, Dundee, UKProf. John W.S. Brown(15) Medical Research Council, MRC Human Genetics Unit, Edinburgh, UKDr. Javier Fernando Cáceres(16) Instituto de Medicina Molecular, Lisbon, PortugalProf. Maria Carmo-Fonseca(17) University of Leicester, Leicester UKProf. Ian Eperon(18) Adam Mickiewicz University in Poznan, Poznan, PolandDr. Artur Jarmolowski(19) University of Aarhus, Aarhus, DenmarkProf. Jorgen Kjems(20) Universidad de Buenos Aires, Buenos Aires, ArgentinaProf. Alberto R. KornblihttDr. Anabella Srebrow(21) Université de Genève, Geneva 4, SwitzerlandProf. Angela Krämer(22) University of Dundee, Dundee, UKProf. Angus Lamond(23) The Chancellors, Masters and Scholars of the University of Cambridge, Cambridge UKDr. Christopher Smith(24) The Hebrew University of Jerusalem, Jerusalem, IsraelProf. Hermona Soreq(25) Centre Européen de Recherche en Biologie et Médicine -Groupement d'Intérêt Economique, Illkirch, FranceDr. James Stévenin(26) Institut National de la Santé et de la Recherche Médicale, Paris, FRANCEDr. Didier Auboeuf(27) Fondazione Centro San Raffaele del Monte Tabor, Milano Italy5
Dr. Davide Gabellini(28) Swiss Institute of Bioinformatics, Biozentrum, University of Basel, SwitzerlandDr. Mihaela Zavolan(29) Eidgenössische Technische Hochschule Zürich, Zürich, SwitzerlandProf. Frédéric Allain(30) International Institute of Molecular and Cell BiologyProf. Janusz Bujnicki(31) Universitat Pompeu FabraDr. Eduardo Eyras(32) University of SouthamptonDr. Diana BaralleEURASNET presents the activity report for the third year of integrated research on alternative splicing. Morethan 60 research papers give testimony to the scientific excellence of the research teams gathered in thisnetwork. Even more encouraging is the fact that about a third of these papers are co-authored by more than justone EURASNET lab. This indicates the remarkable level of integration EURASNET has achieved. Furtherevidence for a truly cooperative approach is the fact that the EURASNET microarray initiative, after securingprivileged access to cutting edge microarray technology, has already provided a standardized platform fornumerous experiments submitted by individual EURASNET members. This technology is a valuable tool totackle those research goals which EURASNET set out to pursue on a genomic scale.Also in 2008, EURASNET research has provided new deep insights into the structure and the function of thesplicing machinery, its components and the regulatory circuits involved. Again EURASNET has been a hotbedfor the development of new innovative approaches to study the peculiarities of the alternative splicingmachinery which is characterized by the intricate interactions of both RNA and protein.Work on disease models and on compounds with therapeutic potential is progressing at a steady speed andjustifies the hope that by the end of the five year period in 2010 many of the overall goals will be fully achieved.EURASNET , in 2008, has been particularly successful in bringing the importance of alternative splicing to thefull attention of the medical community, to the medical practitioner as well as to the diagnostic lab.EURASNET research and the cause it is committed to are presented through an appealing website. The networknow enlists two associates from labs with a medical research focus. A well attended and lively program ofworkshops, intra-workshop sessions and IFMs has provided a further catalytic stimulus to invigorate theexchange of results, ideas and tools within the network as well as with the wider RNA community.6
Page 3 and 4: TABLE OF CONTENTSA. PERIODIC ACTIVI
Page 5: 1 PUBLISHABLE EXECUTIVE SUMMARY EUR
Page 9 and 10: WP7 Molecular characterization of s
Page 11 and 12: To identify protein-protein interac
Page 13 and 14: expressed in a particular tissue. T
Page 15 and 16: Duchenne muscular dystrophy (DMD).
Page 17 and 18: WP21 Reachout to the broader RNA co
Page 19 and 20: 4.1 TABLE OF MILESTONES JPA MONTH 2
Page 21 and 22: Numerous plasmids, constructs, extr
Page 23 and 24: collaboration between EURASNET and
Page 25 and 26: 5.1 WORK PACKAGE REPORTSWork Packag
Page 27 and 28: • Ongoing regular addition of new
Page 29 and 30: 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 and 82:
Publications 2008Author Title Publi
Page 83 and 84:
Author Title Publication EURASNET P
Page 85 and 86:
Page 87 and 88:
Page 89 and 90:
Page 91 and 92:
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 110 and 111:
Page 112 and 113:
Page 114 and 115:
Page 116 and 117:
Page 118 and 119:
Licht K, Medenbach J, Lührmann R,K
Page 120 and 121:
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
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
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J. Beggs has had frequent contact w
Page 152 and 153:
Page 154 and 155:
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 176 and 177:
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 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
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
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283 A unified browser for allknown
Page 242 and 243:
296 Group 12a (Branlant) willuse th
Page 244 and 245:
315 Lamond will use a FLIM-FRET bas
Page 246 and 247:
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
Page 256 and 257:
5. Ensuring DurabilityWorkpackage d
Page 258 and 259:
7. Molecular Characterization of Sp
Page 260 and 261:
8. Genome-wide Analyses of Splicing
Page 262 and 263:
9. Complexity of Spliceosomal Prote
Page 264 and 265:
202 Srebrow will investigate the ro
Page 266 and 267:
12. Mis-splicing and DiseaseWorkpac
Page 268 and 269:
13. Co-transcriptional Mechanisms o
Page 270 and 271:
14. Chemical Biology and Therapeuti
Page 272 and 273:
15. Development of Enabling Technol
Page 274 and 275:
269 IFMs in 20091. “Alternative a
Page 276 and 277:
18. Career DevelopmentWorkpackage d
Page 278 and 279:
20. SMEs and Technology TransferWor
Page 280 and 281:
21. Reachout to the Broader RNA Com
Page 282 and 283:
15.7 WORK PACKAGE LIST (MONTHS 37-5
Page 284 and 285:
ETHZIIMCBUPFSOTON-HGDTOTALJoint Pro
Page 286 and 287:
AMU 5 29 8 42UAAR 5 145 16 1665 29
Page 288 and 289:
Joint Programme of Activities RESEA
Page 290 and 291:
60 month period 18 month periodRequ
Page 292 and 293:
Integration1. Young Investigator Pr
Page 294 and 295:
UCAM-DBIOC 2350,000x1/3 € 50,000x
Page 296:
the management team. Audit costs ar
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