PDF file: EURASNET Annual Report 2008

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• ResearchPersonnelName WP Person-months EurosRosário Nolasco 12 6 6.916,70Sandra Martins 10 5,5 9.012,50José Nuno Pereira 12 3,5 2.650,00Inês Mollet 10 11 14.300,00Houda Hallay 13 1 1.594,56Travel• Sérgio de Almeida attended the Workshop: “Structure and Function of mRNPs”Aarhus, Denmark, 3 rd August to 9 th August 2008.• Ana Rita Grosso presented a poster entitled “Integrating large-scale data from splicing microarrayexperiments” at the 16th Annual International Conference Intelligent Systems for Molecular Biology.Toronto, Canada, July 18-23, 2008.• Celia Carvalho Levy attended the EURASNET Workshop “Imaging the Cell”.Montpellier, France, 17 th to 21 st July 2008.• Professor Dinshaw Patel visited the lab of Carmo-Fonseca to discuss ongoing work with several labmembers.Lisboa, 17 th to 18 th June 2008.• Ana Rita Grosso presented a poster entitled “Genome-wide bioinformatics search for cancerassociatedsplicing misregulation” at the EMBO Conference “RNA and Disease”Rome, Italy, May 31-June 5, 2008.• Maria Carmo-Fonseca attended the EURASNET meeting held in Berlin, 20 th to 23 rd January 2008.169
Participant 17 – Ian C. Eperona) Work performed during the period• WP7: We have characterized the binding of GFP-tagged PTB to alpha-tropomyosin premRNA,in collaboration with Chris Smith (group 23). RNA sequences spanning the regulated exon andthe regulatory sequences in the introns were incubated in nuclear extract, and single molecule TIRFmicroscopy was done to examine the complexes. The number of fluorescent molecules bound to eachRNA molecule was examined by newly-developed statistical methods. Cross-linking was used to showthat the binding of PTB and GFP-PTB was equally probable. RNA substrates carrying mutations invarious PTB binding sites were examined also. The results showed that PTB associated as a definedcomplex, and the length of the polypyrimidine tract affected both the number of proteins bound and theaffinity of binding. Further splicing factors were cloned in expression vectors. The validity offluorescently-tagged U1A was demonstrated by showing that it formed U1 snRNPs and bound to premRNA.• WP14: Continued testing effects on recovery of SMN2 splicing in vitro and in cellsfrom patient fibroblasts when a bifunctional oligonucleotide trans-acting enhancer of splicing (TOES)is altered in respect of its tail length, site of annealing, tail sequence and chemistry; analysis of uptakeby FRET. The binding of activating proteins to the oligonucleotides has been studied, and theefficiency of different activatingsequences on SMN2 exon 7 has been shown to be correlated well with factor binding activity.b) Major cost items with justificationParticipant 1A Type of expenditure Budget total costspersonnel 15167.70consumables 6041.33training 0equipment 1255.57travel 711.34= total direct costs 23175.94+ overhead 4635.19= total eligible costs 27811.13Major cost items• ResearchPersonnelL.P. Eperon [WP 7] 439 hours 11480.99EuroG.E. Eperon [WP 7] 356.6 hours 3686.71EuroFigures include National Insurance contribution paid by university to government, and do not representamount received by employee. Number of hours worked by LPE, who was paid monthly and nothourly, is after subtraction of normal holidays.Dr Eperon was engaged part-time in PCR amplification of cDNA for splicing factors, sequencing,cloning and expression, supporting the single molecule work being done by Dr Cherny; Mr G. Eperoncontinued his in vitro splicing studies on a series of substrates containing putative hnRNP A1 highaffinity sites and to do splicing assays; he also tested the ability of PDMS to make ultra-small subfemtolitreswells; he did X-lining experiments on PTB in support of the single molecule work; hecharacterized the use of displaceable oligonucleotides to trap splicing complexes at defined states.170
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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
Page 120 and 121: Author Title Publication EURASNET P
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
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 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 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
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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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