Investigating the essential roles of Ubiquitin-like molecules and the Ubiquitin Proteasome System
|Lead institution / location||Objectives||Tentative Dates|
|P2-Technion / IL||
2nd-6th March 2014
|P3-MRC / UK||Biophysical and X-ray crystallography.
8th-11th April 2014
|P4-NKI / NL||Peptide modification.
15th-17th October 2013
|P6-LUMC / NL||
|P7b-CRBM / FR||
Visualizing protein-protein interactions in cells.
18th-22nd November 2013
|P8-GOETHE / DE||
Upstream Workshop on Ubiquitin and SUMO.
3rd-7th December 2012
|P9-UNIVDUN / UK||
|P11-GSK / ES||
Screening methodologies for drug discovery (GSK).
Property and Grant Application (Yellow Research)
Commertial Exploitation and Drug Discovery (UBIQUIGENT)
23rd-26th September 2014
P5-UCPH / DK
Mass Spectrometry-based Proteomics and Its Applications in Biology
10th - 14th November 2014
The main objective of this board is to ensure the quality and evaluate the standard of both internal and complementary training across the consortium.
P1-Inbiomed: Manuel S. Rodriguez
P4-NKI: Huib Ovaa
P7B-CRMB: Olivier Coux
P10-GSK: Fernando A. Ramon-Olayo
Skill requirements will be discussed and defined in the first instance by the ESR and the supervisor. The supervisory board will approve proposed individual training programs and suggest complementary scientific training in the institution or, if necessary, with another network partner. Development of complementary skills will be suggested in any of the institutions offering the possibility to take one of the OPEN courses. Overall, the supervisory board will make sure that the quality of the formation is the highest possible and similar for all ESR and most appropriated formation is chosen for all of them.
Some of the secondments are already established in order to successfully achieve the scientific aims.
|Individual Research Project||Partner||Secondment|
|IRP1: Probe molecules and assay reagents to study action in Ub and UBL systems and role of De-Ubiquitylating Enzymes (DUBs); synthetic approaches.||P4-NKI||AP12 Ubiquigent|
|IRP2: Proteasome activation to treat neurodegeneration.||P10-UbiQ||P4-NKI|
|IRP3: Cellular roles of atypical ubiquitin chains.||P3-MRC||P9-Dundee|
|IRP4: Maintaining genome stability by SUMO and ubiquitin.||P6-LUMC||P1-CIC bioGUNE|
|IRP5: In vivo requirements of the UBL modifier SUMO on SALL proteins function during steroidogenesis: D. melanogaster as a model system.||CIC bioGUNE||AP12 Ubiquigent|
|IRP6: Mechanisms of ubiquitylation, deubiquitylation and proteolysis in developmental pathways and under stress conditions.||P2-Technion||P7B-CRBM|
|IRP7: Mass spectrometry analysis of ubiquitylated and SUMOylated proteins.||P5-UCPH||P6-LUMC|
|IRP8: The role of proteasomal Ub receptor Rpn13 in mouse development.||P8-Goethe||P3-MRC|
|IRP9: Role of the SUMO specific ubiquitin ligase RNF4 in the DNA damage response||P9-Dundee||P8-Goethe|
|IRP10: Functional connections between protein SUMOylation and reactive oxygen species.||P7A-IGMM||AP12 Ubiquigent|
|IRP11: The role and regulation of the proteasome regulator PA28?||P7B-CRBM||P2-Technion P7C-CBS|
|IRP12: The role of ubiquitylation in infectious diseases.||P11-GSK||AP12 Ubiquigent|
The consortium can offer to the ESR and ER a broad range of complementary skills training. The complementary skills training listed in the table below are open to all ESR and ER so that every fellow has ample opportunity to follow the complementary skills training of the fellow's choice although it may be offered by another partner in the network. The following complementary skills training are OPEN to all ESR and ER of UPStream and are offered by the partners indicated:
|Complementary skills||Offered by Partners|
|Safety and Biosecurity, Research policy, Presentation skills, Organisational skills, Language skills, Ethics, Teaching and supervision skills||All partners|
|Drug Discovery Methodologies||P11-GSK|
|Drug Discovery Applicable Assays||P11-GSK|
|Entrepreneurship, Project management Commercial exploitation of results||P4-NKI, P10-UbiQ, P11-GSK|
|Grant application writing skills, IPR||Subcontracted to Third Party|
|Intensive Medical Writing Course||P5-UCPH|
|Proposal Writing||P2-Technion, P4-NKI|
|Scientific Writing skills||P4-NKI, P6-LUMC, P9-UNIVDUN|
UPStream meetings will be organized with the following aims:
Students will attend the following meetings
Each institution in the network will provide the following courses to their PhD students (ESR), and they will be open to all the ESR in the network (optional courses).
|P1-CIC bioGUNE||Specific training in confocal microscopy, D. melanogaster genetics using conditional knockdown and over-expression and RNAi technology will be provided. In vivo detection of ubiquitylated or SUMOylated proteins using specific technology will be available.|
|P2-Technion||Specific training in proteasome purification, mitochondria isolation, and how to design experiments for use of mass spectrometry approaches in analysis of ubiqutinome and proteome screens.|
|P4-NKI||Research and teaching in basic and clinical oncology (http://www.ooa-graduateschool.org). The course Scientific Writing skills is regularly updated and offered through the Oncology Graduate School Amsterdam.|
|P5-UCPH||Research on training in the proteomic analysis of ubiquitylated proteins.|
|P6-LUMC||Research on training in the proteomic analysis of SUMOylated proteins.|
|P7A-IGMM and P7B-CNRS||Identifying the proteins whose deSUMOylation is induced by chemotherapy-induced ROS in chemosensitive tumors using the SILAC/MS approach.|
|P8-Goethe University||Training in mouse genetics/physiology, biochemistry, proteomics, cellular biology and crystallography.|
|P9-UNIVDUN||Proteomics with a range of mass spectrometers for different purposes including two triple quads for selective reaction monitoring and identification of post-translational modifications.|
|P10-UbiQ||Will do the course on peptide modification carried out by Dr Ovaa at P4-NKI. as well as a course focused on commercial product development in which the gap between academic discoveries and commercial product is highlighted as well how to bridge this gap.|
|P11- GSK||Specific training in microbiology, cell culture, mass spec proteomics and molecular biology will be provided. Training on drug discovery methodologies and business.|
|AP12-Ubiquigent||Ubiquigent will share its views on commercial exploitation of results by providing a course dedicated to the researchers in this network. Ubiquigent will also organise a dedicated course for those interested in development of drug discovery applicable assays.|