PDF file: EURASNET Annual Report 2008

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Participant 14 – John W. S. Browna) Work performed during the period• WP1During the reporting period the EURASNET website was relocated to SCRI. The website wasre-organised and a team put in place to deliver a new, dynamic website targeting specificgroups of potential end-users. The need for good interactions with other Dissemination WPswas addressed by building close interactions with the Barta group (responsible for PublicUnderstanding of Science) and co-ordinating activities. The new website has been launchedand continues to be developed.• WP6Mihaela Zavolan identified potential mRNA targets of novel, “orphan” snoRNAs from plantsand these are now being analysed by transcript analysis in a mutant.• WP8The three plant labs (Barta, Brown, Jarmolowski) have expanded the alternative splicing RT-PCR panel for examining AS in Arabidopsis. The panel is being used to analyse a range ofmutants in splicing factors (SR proteins) and other genes involved in mRNA biogenesis (e.g.cap-binding proteins, RNA binding proteins involved in circadian clock, nonsense-mediateddecay). In addition, a mutant in the microRNA pathway has been analysed. The effect ofdifferent environmental stresses on alternative splicing in plants is also being analysed usingthe RT-PCR panel and the plant groups have secured EU funding in this area. Importantresults from our analyses are 1) there are many novel and unexpected AS events showing thatmuch more AS occurs than currently estimated; 2) cap-binding proteins can influencealternative splicing of the first intron in a transcript; and 3) around 15% of transcripts areturned over by NMD. This strong collaboration among the three plant labs has alreadyinvolved numerous post-doc and PhD student exchanges which will continue over the nexttwo years. We have also organized an annual meeting of the plant groups to co-ordinate ourresearch efforts in this area. Finally, other plant labs in Europe now collaborate with us to usethe RT-PCR panel clearly demonstrating further translation of EURASNET-sponsoredresearch to the wider RNA community.• WP11We are continuing to prepare over-expression lines of the Arabidopsis PTB-like proteinisoform genes, PTBL1and PTBL3 and to characterize putative knock-out mutants for analysison the Arabidopsis AS RT-PCR panel.• WP21I manage the WP21 workpackage – “Broader outreach to the wider RNA community”. In thereporting period we have continued to built good relations with WP19 – Public Understandingof Science and have taken over WP1 – the EURASNET website. The co-ordination ofactivities has been valuable in generating ideas and gathering information and the websitefacilitates interactions with a wider community of RNA scientists. We have takenresponsibility for gathering information about the many and varied activities of members forthe annual report.165
) Major cost items with justificationParticipant 14 Type of expenditure Budget total costspersonnel 58,714.84consumables 32,828.98training 0.00equipment 5,529.29travel 2,279.75= total direct costs 99,352.86+ overhead 15,512.60= total eligible costs 114,865.46Major cost items• ResearchPersonnelThe main personnel cost in the research component is for a part-time post-doctoralscientist (Dominka Lewandowska).Dr. Dominika Lewandowska [WP 8/11/21]19,063.91 EuroConsumablesMajor consumables costs include sets of fluorescently labelled primers for thealternative splicing RT-PCR system, along with sequencing runs and associatedreagents and chemicals.SequencingChemicals/Enzymes/Laboratory supplies20,000 Euro5,000 EuroTravel• RNA meetings/Workshop UK/WP visitsEquipmentHardware and software for new website2,400 Euro5,500 Euro• Integration (including Integration Manager)PersonnelThe main personnel costs in the website component are the part-time contributions ofthe website team.Website team [WP1]Website design and set-up39,650.93 Euro6,700 Euro• DisseminationRNA meetings/WP1/19/21 meetings166
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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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Page 116 and 117: Author Title Publication EURASNET P
Page 118 and 119: 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 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 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
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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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