Investigating the essential roles of Ubiquitin-like molecules and the Ubiquitin Proteasome System



Lead institution / location Objectives Tentative Dates
P2-Technion / IL

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2nd-6th March 2014

P3-MRC / UK Biophysical and X-ray crystallography.
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8th-11th April 2014

P4-NKI / NL Peptide modification.
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15th-17th October 2013


Proximity Ligation.
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Visualizing protein-protein interactions in cells.
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18th-22nd November 2013


Upstream Workshop on Ubiquitin and SUMO.
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3rd-7th December 2012


Gene Silencing.
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P11-GSK / ES

Screening methodologies for drug discovery (GSK).

Property and Grant Application (Yellow Research)

Commertial Exploitation and Drug Discovery (UBIQUIGENT)
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23rd-26th September 2014


Mass Spectrometry-based Proteomics and Its Applications in Biology

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UCPH Webpage


10th - 14th November 2014

Training Executive Board - TEB


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

Objetives and minimal training requirements


  • To train PhD and postdoctoral students (ESRs and ERs) in research methods and practice by performing well-supervised, high-quality research projects at the forefront of international science in well equipped laboratories
  • To make ESRs aware of the theory, practice, capabilities and limitations of modern techniques in life science research
  • To train students in the generic skills of scientific research i.e. experimental design, data analysis, literature survey, communication skills, teamwork and computer skills
  • To assist students to obtain appropriate employment upon completion of their studies by means of a Personal Training and Career Development Plan
  • To provide an intellectually exciting and supportive work environment.

Essential role of intracellular protein degradation.

The core part of all Individual Research Projects (IRPs) consists of original research, directed towards solving important, novel and open questions. All courses include compulsory taught elements (technical training) in subject specific and generic skills that are delivered throughout the duration of the course. In addition to training in specific disciplines ESRs are also encouraged to participate in additional technical as well as in complementary skills training.


The partners have agreed to formulate a common system for defining the workload of the PhD curriculum under the UPStream training network. We have opted to express the training curriculum in analogy to the European Credit Transfer Systems, ECTS. Using such credit system makes the teaching and learning more transparent across our network. It aids us in the design of our PhD curriculum as well in the quality assurance by supervisors and supervisory board. In order to apply a common credit system across our network we have agreed to standardize the workload of our PhD training to 1600 hours for an academic year and based on that we have agreed that one training credit corresponds to 30 hours of work. The number of working hours set are only set as a means to express the training credits, in practice this may mean that there may be differences in working hours between the countries due to national laws.

PhD curriculum

The PhD curriculum within the UPStream network consists of: training through original research, secondment, technical mandatory training, technical additional training and complementary skills training. The relative workload of the training elements is indicated in the table below. Each training element is detailed bellow, except for training through original research, which is explained in detail under each Individual Research Projects.

PhD Curriculum Training Elements Credits
Training through original research Individual Research Project 75
1 Secondment 25-30
Training by Education Technical Mandatory Training 27-32
Additional Technical Training 20
Additional Skills Training e.g. Project Management, Product Development, IPR, Language & culture etc. 8
Total   160

Personal Training and Career Development Plan

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.

Additional Scientific / technical skills

The following partner institutions have courses OPEN to the technical formation of ESRs and ERs of UPStream:

1) Confocal Microscopy: P6-LUMC: P2-Technion, P1 bioGUNE
2) Surface Plasmon Resonance: P1-CICbioGUNE, P2-Technion,
3) SILAC: P2-Technion: P10-Dundee U.
4) Cell imaging: P8 CRBM, P7 IGMM.


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

Complementary skills

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

Network-wide Training

UPStream meetings will be organized with the following aims:

  • To give the opportunity and train PhD students (ESR) to present their work,
  • To present to the rest of the network the progress of each PhD or postdoctoral students (ESR/ER)
  • For the evaluation of the scientific quality of the formation by the mentoring committee

Students will attend the following meetings

  • First Project meeting: UCPH, Copenhagen (Autumn 2013)
  • Second Project meeting: GSK, Madrid (Autumn 2014)
  • Third Project meeting: IGMM, Montpellier (Autumn 2015)

Local Technical Training

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 ( 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.