Edinburgh Proteomics Club

  

 

We have recently (from May 2009) started monthly meetings of the Edinburgh Proteomics Club (EPC). The initial focus is to establish a network among interested researchers from various groups across different Schools and Colleges in the Edinburgh University. Currently, The School of Biology with the Wellcome Trust for Cell Biology and the Centre for Systems Biology at Edinburgh and the School of Chemistry are endorsing EPC. 

 

April 2010

There was an EPC meeting in Room S7.20, Michael Swann Building at 4:00-5:00pm, 29th April (Thursday).

Lysimachos Zografos (School of Informatics): Networks of Cognition: Isolating, Modeling and Comparing Protein Complexes of the Postsynaptic Density

The postsynaptic density (PSD) is a multi-protein complex consisting of over 1000 proteins, which underlies molecular computation in the brain and is involved in cognition and mental disease. We have previously isolated and modeled mouse PSD (mPSD) complexes using a workflow that involves proteomic isolation and identification of complexes and also reconstruction of their protein-protein interaction network models, enriched with functional annotation and statistical analysis. The mPSD model raised several questions about the evolution, not only of the sequences of the constituent parts but the network’s architecture and topology. In order to answer these questions we have now started modeling the fruit fly’s PSD (fPSD) using the same workflow. In this talk I will present an overview of the mPSD results, current progress in the cataloguing and modeling of the fPSD and also our comparative interactomics approach, that is based on function and topology rather than protein sequences.

 

March 2010

There was an EPC meeting in Room S7.20, Michael Swann Building at 4:00-5:00pm, 11th March (Thursday).

Dr. Matt Brook (Centre for Cardiovascular Science): Poly(A)-binding proteins are highly post-translationally modified: First insights into PABP PTM function

 

January 2010

January EPC meeting has been cancelled and rescheduled to 4th February in Room S7.15, Michael Swann Building at 4:00-5:00pm. 

Dr. Perdita Barran (Chemistry Department): Ion-Mobility Mass Spectrometry of Peptides: Switches, Amyloids and Antimicrobials 

 

December 2009

The last EPC meeting for 2009 was in Room S7.15, Michael Swann Building at 4:00-6:00pm, 16th December (Wednesday).  Dr. Gill has presented a fascinating talk before a social networking/chatting event. The refreshments have been generously provided by the Wellcome Trust Centre for Cell Biology. 

Dr. Andrew Gill (Roslin Institute): Molecular Phenotype of Loss of Prion Protein Function

Transmissible spongiform encephalopathies (TSEs) are disease associated with misfolding of the prion protein, leading to neuronal loss, astrogliosis and deposition of prion protein aggregates in the brain. The diseases include scrapie in sheep, BSE and CJD and they are invariably fatal. We have no reliable pre-mortem diagnostic test, no cure and we still understand little about the causes of disease. However, we know that the prion protein is central to disease, since transgenic mice lacking the protein do not succumb to infection. An underlying question in TSEs, and in other protein misfolding diseases, is whether the protein aggregates that accumulate during disease cause neuronal loss directly through toxic mechanisms, or whether loss of the normal function of the prion protein (as the protein gets incorporated into growing aggregates) results in neuronal cell death. Within the group we have a range of projects investigating molecular aspects of prion diseases and I will touch briefly on a few of these. However, to investigate whether prion protein loss of function is important in TSE disease we have been using knockout mice to undertake post-genomic studies of differential gene and protein regulation during ageing, relative to age and sex matched wildtype mice. The project is reaching the final stages and I will go through our methodology and give an indication of the findings so far.

 

November 2009

There was an EPC meeting in Room S7.15, Michael Swann Building at 4:00-5:00pm, 18th November (Wednesday).

Dr. Tatsiana Auchynnikava (Robin Allshire’s Lab): Strategies for Isolation of Subkinetochore Chromatin Complexes

Introduction: Knowledge of the composition of protein complexes is a key to understanding cellular processes. Immunoaffinity purification followed by mass-spectrometry based proteomics is a widely used approach to characterise protein complexes.  We employ proteomic analysis to describe the interactome the sub-kinetochore chromatin of Schizosaccharomyces pombe. Commonly used purification and sample preparation strategies have their limitations, especially in the case of low-abundant and unstable complexes.  Improving yield of the purifications is important to achieve maximum coverage of the protein-protein interactions with proteomic analysis. Currently we are modifying existing protocols to preserve rare native complexes to allow their isolation with minimal losses. Progress in the method development is going to be discussed.     

Dr. Grzegorz Kudla (David Tollervey's Lab): Mapping RNA Structures by UV Crosslinking and Deep Sequencing

 

October 2009

There was an EPC meeting in Room S7.15, Michael Swann Building at 4:00-5:00 pm, 22nd October (Thursday). Two speakers presented interesting topics

Miss Claudia Bicho ( Ken Sawin’s Lab): A Robust SILAC Method for Fission Yeast

Dr. Victor Neduva ( Mike Tyers’s Lab): Exploring Yeast Kinome: methods and models

 

June 2009

The EPC met jointly with the Mass Spectrometry User Club in Room S7.20, Michael Swann Building at 4pm, Thursday 11th June. Representatives from individual groups interested in Mass Spectrometry and/or Proteomics gave a brief introduction on their research topics to about 55 participants. The speaker list is as below.  After the talks, a poster session of about 20 posters in the Swann foyer gave an opportunity to engage each other informally (refreshments provided generously by the Wellcome Trust Centre for Cell Biology). 

Dr. Juri Rappsilber                            Wellcome Trust Centre for Cell Biology

Prof Charles ffrench-Constant             MRC Centre for Regenerative Medicine 

Dr. Jurgen Haas                                Division of Pathway Medicine 

Dr. Thierry Le Bihan                          Centre for Systems Biology at Edinburgh

Dr. Juan Zou                                     Wellcome Trust Centre for Cell Biology 

Dr. Andrew Cronshaw                        School of Biological Sciences 

Dominic Campopiano                        School of Chemistry, Campopiano Group 

Martin De Cecco                               School of Chemistry, Barran Group     

Adam Stokes                                    School of Chemistry, SIRCAMS

May 2009

The First Meeting was in the School of Chemistry with about 25 participants. Dr. Dave Clarke delivered a presentation on Electron Capture Dissociation of proteins.