MRC PPU News
Former Members of the MRC-PPU Marry
17 December, 2014
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Edmond Wong and Huei-Ting Yang

Huei-Ting Yang, a Ph.D. Student in Philip Cohen's lab from 2004-2008 and Edmond Wong, a postdoc in Daan van Aalten's lab and then Philip Cohen's lab from 2007-2009 were married in September in two ceremonies held in Taiwan and the UK. Huei-Ting is currently a Senior Development Scientist at Oxford Immunotec, and Edmond is a senior scientist at Immunocore, another biotech company based in Oxford in the UK. This is the 14th time that a student or postdoc in Philip Group has married another student or postdoc in the MRC-PPU. So if you want to do great science but have not yet met the right person please consult our recruitment page on how to apply!




 

Gerrit Daubner awarded EMBO Long-term Fellowship
15 December, 2014

​Many congratulations to Gerrit Daubner, a postdoctoral researcher working in Dario Alessi’s group, who has been awarded a prestigious personal long-term EMBO Fellowship.

Gerrit’s research aims to elucidate the molecular mechanism by which the WNK kinases are regulated. WNK kinases are master regulators of ion homeostasis and blood pressure. They are capable of sensing changes in extracellular ion concentrations and control the activity of downstream SPAK and OSR1 protein kinases, which in turn modulate the function of critical ion co-transporters. The importance of the WNK signalling pathway is illustrated by the finding that mutations in seven components of this pathway have been linked to hypertension disorders in humans.

Prior to working in Dario Alessi’s group, Gerrit undertook his PhD research training in the laboratory of Frédéric Allain at the ETH Zurich. There he performed structural and functional studies of RNA-binding proteins involved in post-transcriptional regulation.

Congratulations as well to Lina Herhaus who recently completed her PhD research in the laboratory of Gopal Sapkota, and who has also been awarded an EMBO Fellowship to work in the laboratory of Ivan Dikic at Goethe University Medical School, Frankfurt, Germany.




 

Philip Cohen receives the Albert Einstein World Award of Science in Helsinki on 17 November 2014
12 December, 2014
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Philip signs the book of recipients of the Albert Einstein Award, watched by Nobel Laureate Edmond Fischer, President of the World Cultural Council and Tuula Teeri, the President of Aalto University, Helsinki, who hosted the event.

Philip Cohen received the 2014 Albert Einstein World Award of Science from the World Cultural Council at a ceremony at Aalto University Finland on 17 November 2014. The award was made by the World Cultural Council’s Interdisciplinary Committee including eminent scientists from all five continents.

The prize, which consists of a diploma, and commemorative medal and cheque for ten thousand US dollars, has been awarded for “his 40-year outstanding and continuing scientific career devoted to studying and establishing the profound importance of protein phosphorylation in regulating almost every physiological process. Professor Cohen's achievements meet the criteria for the Albert Einstein World Award of Science most closely in respect to bringing "true benefit and well-being to mankind" in their importance to the development of drugs and treatment with global impact. Professor Cohen’s pivotal contribution has been to elucidate a major section of the insulin signal transduction-signalling pathway, essentially from scratch, starting at a time when virtually nothing was known about cell signalling. This was to be based on his dissection of protein kinase dependent cascades, which are the major intracellular components of hormonal signalling networks. His research has raised Dundee University to one of the leading academic institutions in his field of this study. Professor Cohen has made decisive contributions to the growth and international reputation of life sciences at the university and to the development of a life sciences cluster in the city, which now accounts for 16% of its economy. In fact, the College of Life Sciences has, for several years, been voted one of the best scientific environments in the world in which to work. Throughout his career Philip Cohen has been an exceptional mentor of talented young researchers. More than one hundred PhD students and postdoctoral scientists have trained in his laboratory over thirty-eight years, with the vast majority now working in senior roles as academic research leaders.”
To read the full citation click here.




 

BBSRC Industrial CASE studentship awarded to Matthias Trost
12 December, 2014

Matthias Trost has been awarded a BBSRC Industrial CASE studentship to develop novel methods for deep proteome analysis in collaboration with Thermo-Fisher Scientific.

This 4-year studentship which is only open to UK nationals or EU citizens resident in the UK for more than three years, will aim to develop novel leading-edge tools to identify and quantify >10,000 proteins in cell lysates in a single, short experiment.

The successful candidate will deploy state-of-the-art chromatography and mass spectrometry technologies to investigate exciting questions in macrophage biology.

For more information and how to apply click here




 

Parkinson’s UK 3-year PhD Prize Studentship awarded to Miratul Muqit
4 December, 2014

Miratul Muqit has been awarded a Parkinson's UK studentship to investigate the functions of the PINK1 kinase in Parkinson’s disease.

This 3-year studentship will aim to identify and characterize novel PINK1 substrates and builds on the work of a previous Parkinson’s UK PhD student, Chandana Kondapalli, who identified the first PINK1 substrate, Parkin.

The successful candidate will deploy state-of-the-art technologies to investigate and characterize newly identified substrates of PINK1 and determine how these are linked to neurodegeneration in Parkinson’s.

For information on how to apply click here




 

J Macdonald Menzies 4-year PhD Prize Studentship in Parkinson’s disease awarded to MRC researchers
4 December, 2014

The J Macdonald Menzies Charitable Trust have awarded Miratul Muqit and Dario Alessi funding to support a new Prize studentship to investigate the molecular mechanisms of Parkinson’s disease.

This 4-year studentship will build on the ground breaking studies of the first J Macdonald Prize student, Agne Kazlauskaite, who has elucidated the function of the PINK1 protein kinase, discovering and characterizing its key substrates including the E3 ligase, Parkin and ubiquitin.

The successful candidate will deploy state-of-the-art technologies to investigate how this signalling pathway is critical for prevention of Parkinson’s including using highly sensitive antibodies to the key components of this pathway in patient-derived cells and tissues.

For information on how to apply please click here.




 

Claire Eyers promoted to Professor.
25 November, 2014
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Professor Eyers with her children on the beach at Formby, near Liverpool

The news has just come through that Claire Eyers (nee Haydon), a Ph.D. student in Philip Cohen's lab in the MRC-PPU from 1998-2002, has been promoted to a Professorship in the Department of Biochemistry at the University of Liverpool.

Following the award of her Ph.D. in 2002, Claire received a Fellowship from the American Heart Foundation to work with Natalie Ahn at the University of Colorado, Boulder, USA, where she studied combinatorial signaling between MAP kinase pathways using phospho-proteomic technologies. She returned to the UK in 2004 to become a Postdoctoral Research Associate in the Department of Chemistry at the University of Manchester working in Simon Gaskell’s laboratory. In 2007, Claire was awarded an independent Dorothy Hodgkin Research Fellowship from the Royal Society and in 2009 she was made the Acting Director of the Michael Barber Centre for Mass Spectrometry at the University of Manchester. She was appointed Lecturer and then Senior Lecturer in 2012, and in 2013 moved to the Department of Biochemistry at the University of Liverpool where she was promoted to a Readership. Claire’s meteoric promotion through the UK University system is all the more remarkable because she took three separate six month periods of maternity leave between 2005 and 2009 following the birth of her three children Sam (8), Evie (7) and George (5).

Claire is married to Pat Eyers, also a Ph.D. student in Philip’s lab from 1996-2000. Pat is currently a Reader in Biochemistry at the University of Liverpool.




 

MRC-PPU brings leading experts and the public together to discuss the Ageing Brain
19 November, 2014
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L-R: John Starr, Karen Petrie, Elaine Shemilt, Fiona Ross, MIratul Muqit, Guy Fletcher

As part of this year’s Dundee Science Festival the MRC-PPU hosted an interactive panel discussion on November 13th. A dark and stormy evening was illuminated within the university’s Dalhousie Building by a lively evening in which an eclectic mix of experts provided the 80+ members of the public with some genuine food for thought. The event, entitled The Ageing Brain: A Risky Route to Wisdom?, provided a genuine tête a tête involving panellists and the public.

The panellists, whose diversity matched the wide range of questions, included neurologist Miratul Muqit MD, PhD (MRC-PPU), artist Elaine Shemilt FRSA, FRGS (University of Dundee), computer scientist Karen Petrie PhD (University of Dundee), philosopher Guy Fletcher PhD (University of Edinburgh) and NHS consultant John Starr MD, FRCP (Co-Director, University of Edinburgh Centre for Cognitive Ageing).

The event kicked off with each panellist attempting to convince the public that ageing was either a good or bad thing. The ensuing discussion, led by award-winning political journalist Ms. Fiona Ross, OBE, was a whirlwind of commentary ranging from questions about health (what is happening inside the brain when it ages?) to the practical (why can’t computer chips be designed to help those brains that are ailing?) and philosophical (can our perceived state of happiness affect our brains molecularly?). The impact of neurodegenerative diseases in aged populations was a dominant theme throughout the discussion and research undertaken at the MRC-PPU by several groups, including that of Dario Alessi, Helen Walden and Miratul Muqit, to better understand these disorders was highlighted.

And so were we truly any the wiser about ageing and the brain? Judging by the discussions that followed, many were inspired by the evening whilst for others the debate will continue. One thing is clear and that is that we need better understanding of the molecular changes that occur in the brain with ageing and how that is linked to neurodegenerative disease. The research being pursued at the MRC-PPU may one day provide answers to this question, and provide hope that we can all enjoy growing older and wiser.




 

The MRC-PPU at The Dundee Science Festival!
18 November, 2014

What do science and fun have in common? A lot it turns out – as visitors abundantly discovered on their recent visit to The Dundee Science Centre for Family Fun Day on November 2nd, all a part of 2014 the Dundee Science Festival.

Scientists from the MRC-PPU and University of Dundee College of Life Sciences were there in full-force to inform the public about the studies that are so critical to moving forward research around human diseases that affect millions – including cancer and neurodegenerative disease such as Parkinson’s disease. As a part of the one of the events organized by the MRC-PPU - The Wonders of the Brain: Big and Small! - visitors were encouraged to partake in a trivia challenge, all as they journeyed through the exhibit where they learned about the brain, touched a squishy example (made of gelatin, of course!), viewed models from different species, and evaluated example MRIs and illustrations that highlighted changes that occur during disease. The games that were a part of this exhibit were also a great hit as children matched neurotransmitter ‘vesicles’ with the proper receptor, made neurons out pipe-cleaner, made their very own thinking caps and ‘trained their brain’ using memory and motor games.

In Help the Scientists Beat Cancer! children were encouraged to learn about different kinds of cells (and even made their very own to take home) before moving on to discovering what makes cancerous cells differ from normal ones and helping to destroy them. This concluded with the youngsters identifying creative ways to stop ‘bad proteins’ inside cells that often turn normal healthy cells into cancer cells. They quickly discovered that it’s not so easy to do when many of the bad proteins are similar to good proteins one would not want to stop. In the end, they prevailed and were able to create structures that selectively targeted these bad proteins – and hopefully came away with a better understanding and appreciation for the research path that many of the volunteers are treading in their pursuit to help in the fight against cancer and other diseases.

Volunteers for the 2014 Dundee Science Festival from The MRC-PPU and University of Dundee included: Kirsten Airey, George Allen, Arno Alpi, Florence Chang, Giuliana Clemente, Claudia Conte, Tim Cummins, Sonal Das, Laura Feeney, Rosalia Fernandez-Alonso, Alexandra Hale, Thomas Hochdorfer, Axel Knebel, Atul Kumar, Hannah Leech, Olivia Lombardi, Daniel Mariyappa, Tom McWilliams, Villo Muha, Miratul Muqit, Michael Munson, Shalini Pathak, Laia Pedro-Roig, Mark Peggie, Katy Petherick, Nicola Philips, Catherine Rodger, Sam Strickson, Olga Suska, Rachel Toth, Josh Wong and Ning Zhang. Without their suggestions, insight and investment in time, these events would not have been possible.




 

SIK inhibitors take a step closer to the clinic
10 November, 2014

James Ozanne, an undergraduate student from the University of Bath working under the direction of Kristopher Clark, has discovered that, in addition to their anti-cancer properties, the drugs Bosutinib and Dasatinib also possess potent anti-inflammatory actions by switching off a family of enzymes called the SIKs. These findings suggest that Bosutinib and Dasatinib could potentially be re-purposed for the treatment of chronic inflammatory and autoimmune diseases.

A major focus in the Clark lab is to identify new ways to tackle diseases of the immune system such as rheumatoid arthritis and lupus. To this end, the lab recently uncovered a key role for the SIKs in promoting inflammation (PNAS 2012, vol.109 p.16986-16991). Treatment of macrophages with compounds that block the activity of these enzymes leads to a dramatic increase in the production of beneficial anti-inflammatory cytokines (IL-10, IL-1ra) and a suppression of toxic pro-inflammatory cytokines (TNFα, IL-12, IL-6). This dual activity of compounds that switch off the SIKs have made them attractive targets for the treatment of inflammatory diseases. Unfortunately, none of the currently available compounds have the required drug-like properties to test this idea.

James therefore sought to identify clinically-approved drugs that could block the SIKs, in addition to their main target. Many anti-cancer drugs switch off enzymes known as protein tyrosine kinases. The lab previously noticed that these enzymes share a special feature with the SIKs, which could allow some drugs to bind to members of both families. By testing a number of different anti-cancer drugs, James found that Bosutinib and Dasatinib could block the SIKs, thereby converting macrophages to an anti-inflammatory state. James was able to further show that the effects of Bosutinib and Dasatinib were the result of blocking the SIKs, and not protein tyrosine kinases, because he engineered macrophages to express a mutant of the SIKs that does not bind to these drugs and found that Bosutinib and Dasatinib could not switch this macrophage population to an anti-inflammatory state.

Our findings, in combination with the current use of Bosutinib and Dasatinib in the clinic and the observation that Dasatinib is effective at suppressing arthritis and atopic dermatitis in pre-clinical models, make us optimistic that drugs which selectively turn off the SIKs will be well-tolerated in human patients and be efficacious in the treatment of chronic inflammatory and autoimmune diseases. We propose that in the absence of such compounds, Bosutinib and Dasatinib should be considered for the treatment of debilitating inflammatory diseases, in particular, those diseases for which there are no reasonable current treatments.

Click here to access the complete article published in the Biochemical Journal.




 

The end of chromosome replication
30 October, 2014

One of the most striking features of chromosome replication in eukaryotic cells is that it only happens once in each cell cycle. This makes DNA replication very different to transcription, during which each gene is copied many times into RNA. Whereas an RNA polymerase can melt double-strand DNA on its own, a DNA polymerase must wait for its template to be provided by the action of a DNA helicase, which unwinds the DNA duplex and represents a key focus for regulation. The replicative helicase in eukaryotic cells is highly complicated and is controlled in an exquisite fashion, so that it only gets one single opportunity to unwind each stretch of the genome during every round of chromosome replication. In a new paper just published in Science, Marija Maric from Karim Labib’s group has identified an exciting new mechanism by which the eukaryotic replicative helicase is regulated.

The essential helicase at eukaryotic forks is a multimeric complex known as ‘CMG’ or Cdc45-MCM-GINS. The catalytic core of the helicase is formed by the six Mcm2-7 proteins, which are loaded around DNA in an inactive form during the G1-phase of the cell cycle. Once cells enter S-phase, the loaded Mcm2-7 hexamers are activated by recruitment of two missing components known as Cdc45 and ‘GINS’ (itself a complex of four small proteins). The activation process is driven by cyclin dependent kinase and Cdc7 kinase, which phosphorylate the Mcm2-7 helicase core, as well as two of the three loading factors that recruit GINS and Cdc45 to origins of replication. Work over the last decade has shown that the helicase activation mechanism is conserved from humans to yeast, indicating that it represents a universal mechanism for the initiation of chromosome replication in eukaryotic cells.

Once activated, the CMG helicase is very tightly associated with DNA replication forks and must never be displaced, as reloading or reactivation cannot occur until the subsequent cell cycle. Nevertheless, when two converging replication forks from neighbouring origins meet each other, replication is terminated in that region of the genome, and disassembly of the CMG helicase is likely to be the key regulated step in replisome dissolution. Until now, nothing was known about the underlying mechanism of helicase disassembly.

Following up on an original observation from a former postdoc in Karim’s group, Giacomo de Piccoli, Marija showed that the CMG helicase is ubiquitylated, specifically on its Mcm7 subunit, in a reaction that only occurs at the end of chromosome replication. Ubiquitylation of the helicase leads to a disassembly reaction that requires the Cdc48/p97 segregase, which probably acts by pulling the ubiquitylated Mcm7 subunit out of the CMG helicase, causing the rest of the complex to fall apart. The E3 ligase responsible for this process is called SCFDia2 and was identified by Timurs Maculins during his PhD studies in Karim’s group. Tim showed that SCFDia2 is essential for disassembly of the CMG helicase at the end of S-phase, consistent with Marija’s data. These findings raise many interesting questions that will drive new projects in the replication field over the coming years. In addition to elucidating fully the mechanism of helicase disassembly, a key issue will be to address how the process is regulated so that it never occurs before the termination of replication, but then always happens. By analogy with the initiation of chromosome replication, it will be important to explore whether helicase disassembly also involves a universal mechanism in diverse eukaryotic species, which helps to preserve genome integrity in proliferating cells. Whatever the answer, it now seems clear that the end of chromosome replication is regulated just as carefully as the start.

To read a copy of Marija’s paper that has just been published, click here.




 

Vicky Cowling Awarded Prestigious British Society for Cell Biology Medal
30 September, 2014
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Vicky Cowling in the lab

MRC-PPU PI Vicky Cowling has been awarded the inaugural Women in Cell Biology Early Career Award Medal by the British Society for Cell Biology.

The Medal has been established to mark the 50th anniversary of the founding of the British Society for Cell Biology. It will be an annual honour awarded to an outstanding female cell biologist who has started their own research group in the UK within the last seven years.

Vicky’s research aims to discover new ways to suppress the growth and proliferation of cancer cells by targeting protein translation. Vicky has recently made a number of significant breakthroughs that have resulted in a better understanding how the machinery that controls mRNA cap formation is regulated by signalling pathways and oncogenes. Vicky is also investigating whether developing compounds that target the apparatus that controls the mRNA Cap formation could employed as a novel therapeutic strategy to better treat cancer in the future.

Upon receiving news of the prize Vicky said, “I am delighted that our research has received this recognition from the British Society for Cell Biology.”

Last year Vicky was awarded a Medical Research Council Senior Non-Clinical Fellowship (£2.5million over seven years) to support her research. Vicky’s research has also received recognition through the award of a highly sought after EMBO Young Investigator Prize (EMBO-YIP) and a Lister Institute Prize.

Announcing the award, Professor Jordan Raff, President of the BSCB, said, “While the concept of women-only prizes is controversial, it is widely acknowledged that a disproportionately large number of talented, young, female scientists leave science to take up other careers. We hope that this award will help raise the profile of some of our most promising young stars at a crucial stage in their career and that the awardees will serve as inspiring role models for the next generation of female cell biologists.”

MRC-PPU Director Dario Alessi said “I am delighted that Vicky has been awarded this great accolade that is richly deserved. This is a great reflection of the strength and calibre of our Unit's researchers."

Dr Cowling will be presented with the medal at the BSCB/BSDB Annual Spring Meeting in Warwick in April 2015, when she will deliver the inaugural Medal Lecture.




 

Characterisation of VPS34 inhibitor reveals PtdIns 3-P binding SGK3 protein kinase is downstream target of Class III PI-3 kinase
1 September, 2014

Phosphoinositide 3-kinases (PI3K) phosphorylate the 3’-position hydroxyl of the D-myo-inositol head group of phosphatidylinositol (PtdIns) to generate 3-phosphoinositides that play critical in orchestrating a wide range of biological responses including controlling cell growth, proliferation and intracellular trafficking.

There are three different Classes of PI3Ks termed Class I, Class II and Class III. The most studied enzymes comprise the four members of Class I PI3Ks (p110alpha, p110beta p110gamma and p110delta) family. These phosphorylate PtdIns(4,5)P2 at the plasma membrane to generate the signalling second messenger PtdIns(3,4,5)P3 in response to agonists that trigger activation of growth factors, Ras or G protein coupled receptors.

Excitingly, the first PI3K inhibitor termed Idelalisib, developed by Gilead Sciences that targets the p110 delta isoform, has recently received FDA approval. Idelalisib is designed to be used combination with rituximab for chronic lymphocytic leukaemia and predicted to generate 1.3 billion dollars in sales. The expectations are that this drug and other PI3K inhibitors being developed will also be useful in treating solid tumours.

In contrast, the roles of the 4 isoforms of the Class II and single isoform of Class III PI3K isoform (also termed Vps34), in comparison to Class I PI3Ks, are much less well understood. Their function seem to be to phosphorylate PtdIns in order to generate PtdIns(3)P. Evidence to date indicates that Vps34 plays an important role in controlling vesicular protein sorting.

Ruzica Bago, a postdoc in Dario Alessi's lab, in collaboration with a number of other researchers including two Phd Students [Nazma Malik (Alessi lab) and Michael Munson (Ganley lab)] as well as AstraZeneca researchers (Richard Ward and Darren Cross), was interested in characterising a pharmacological inhibitor that would permit the the role of the Class III PI3Ks to be better investigated. Ruzica was also curious to determine whether VPS34 played a role in regulating the activity of the only protein kinase in the cell known to interact with PtdIns(3)P, namely the serum and glucocorticoid protein kinase-3 (SGK3).

To undertake this project Ruzica first painstakingly analysed the potency and specificity of a number of potential VPS34 inhibitors that have been reported in the patent literature. This led to the identification of a compound that we termed VPS34-IN1, which inhibited recombinant Vps34 with nanomolar potency, but did but does not significantly inhibit the activity of 340 protein kinases or 25 lipid kinases tested that include all isoforms of Class I as well as Class II PI3K. Ruzica was able to demonstrate that VPS34-IN1 when added to cells, rapidly reduced endosomal PtdIns(3)P levels within 1 min of drug treatment.

Ruzica then established that mutations in SGK3 that prevented PtdIns(3)P-binding also ablated SGK3 kinase activity by suppressing phosphorylation of the T-loop (PDK1 site) and hydrophobic motif (mTOR site) residues. Ruzica found that VPS34-IN1 in cells induced a rapid ~50-60% loss of SGK3 phosphorylation. Furthermore, Ruzica also found that Class I PI3K inhibitors (GDC-0941, BKM120) that do not inhibit Vps34, suppressed SGK3 activity by ~40%. Combining VPS34-IN1 and GDC-0941 reduced SGK3 activity ~80-90%.

We have interpreted these data to suggest that SGK3 phosphorylation and hence activity is controlled by two pools of PtdIns(3)P. The first is produced through phosphorylation of PtdIns by Vps34 at the endosome. The second is due to the conversion of Class I PI3K product, PtdIns(3,4,5)P3 to PtdIns(3)P, via the sequential actions of the PtdIns 5-phosphatases (SHIP1/2) and PtdIns 4-phosphatase (INPP4B) (See Figure).

We believe that VPS34-IN1 will be a useful probe to delineate physiological roles of the Vps34.

We propose that monitoring SGK3 phosphorylation and activity could be employed as a biomarker of Vps34 activity, in an analogous manner by which Akt is used to probe cellular Class I PI3K activity.

Finally, it would be interesting to explore whether combining Class I (e.g. GDC-0941) and Class III (e.g. VPS34-IN1) PI3K inhibitors, could be used as a strategy to better analyse the roles and regulation of the elusive Class II PI3K.

To read a copy of Ruzica’s paper that has just been published click here.




 

Researchers develop new method for drug discovery in the ubiquitin field
27 August, 2014
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Stella Ritorto

The potential to develop new drugs to target a class of enzymes which are implicated in major diseases such as cancer and neurodegenerative conditions has been boosted with the development of a new drug discovery method in a research effort performed by Stella Ritorto in Matthias Trost's laboratory

Stella and her collaborators have been examining the class of enzymes called deubiquitylases (DUBs). Around 90 DUBs have been identified in the human genome and they are active in almost every process in cells.

Drugs that target components of the ubiquitin system are predicted to become of major importance to the pharmaceutical industry in the future. However, until now it has proved difficult to carry out sufficiently detailed and accurate mass testing of compounds against specific DUBs.

Now the team led by Dr Matthias Trost in the MRC-PPU with collaborators from the Dario Alessi lab (MRC PPU) and the Nathanael Gray lab (Harvard Medical School) have developed a new drug discovery method using MALDI TOF mass spectrometry that will allow greater analysis of the activity of specific DUBs and how they react to treatment with drug compounds.

“This is the first method which allows us to carry out high-throughput screening of DUBs, which is essential if we are going to be able to identify new drug targets and develop new drugs. This is why major pharmaceutical companies, many of whom we work with, are very excited about this because it opens new avenues of drug development in this area,” said Dr Trost.

Dario Alessi, Director of the MRC-PPU and a co-author on the paper stated “Stella Ritorto has worked incredibly hard and done an awesome job in setting up the MALDI-TOF DUB assay. The key advantage of Stella’s assay is that it enables DUB activity to be assessed in a high-throughput manner for the first time employing more physiological non-chemically modified di-ubiquitin substrates, in contrast to existing methodology that makes use of artificial chemically modified ubiquitin derivatives. There is increasing interest in developing specific DUB inhibitors not only to better treat diseases such as cancer, Parkinson’s and immunological disorders, but also to explore the biological processes that these fascinating enzymes control. I hope that the MALDI-TOF DUB assay that Stella has developed will enable researchers to easily undertake high-throughput screens for DUB inhibitors employing physiological unmodified di-ubiquitin substrates. Just as importantly, it will enable the substrate specificity of the DUB inhibitors to be rapidly assessed against a panel of ~35 other DUBs. This should accelerate efforts to develop highly selective and potent DUB inhibitors. We would urge any group with an interest in developing specific DUB inhibitors to get in touch with us to discuss the evaluation of the selectivity of their compounds using the MALDI-TOF DUB assay”

The results of the research are published today in Nature Communications.




 

MRC-PPU football team
20 August, 2014

Earlier this month the MRC-PPU football team participated for the first time in the College of Life Sciences football tournament, playing three matches:

Game 1 against the Division of Molecular Microbiology (MMB) - who just happen to be last year's champions - resulted in a 1-1 draw, Game 2 against the Division of Biochemistry & Drug Discovery (BCDD) saw the opposition win 3-2, and finally Game 3 against the Division of Cell & Developmental Biology (CDB) resulted in a disappointing 4-0 loss. However, this disappointment was lessened when CDB went on to take first place overall in the tournament.

Team Captain Bob Gourlay had two assists and one goal, and Roy Zhang scored two goals. Despite the results the team was very happy with their performance, thoroughly enjoyed all their games, and are already looking forward to next year.

Image:
Front row, L-R: Alba Gonzalez (Trost lab), Jinwei Zhang (Alessi lab), Jiazhen (Roy) Zhang (Cohen lab), Marianne Schimpl (Van Aalten lab)
Back row, L-R: Ning Zhang (Alessi lab), Thomas McWilliams (Muqit lab), Bob Gourlay (Team Captain, Trost lab), Michael Munson​ (Ganley lab), Olawale Raimi (Van Aalten lab)




 

Professor Sir Philip Cohen gives talk in Parliament
18 August, 2014
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Tricia and Philip debate medical research with "Prime Minister Sir Winston Churchill" over dinner in the House of Commons, August 16th 2014

On the evening of August 16th Philip Cohen gave the closing lecture of the 8th International Workshop on Waldenstrom’s Lymphoma in the Churchill rooms of the Houses of Parliament in London.

Waldenstrom’s lymphoma is caused by mutations in the protein MyD88, and 95% of the patients who are afflicted by this disease express the same mutant in which the leucine residue at position 265 is changed to proline. MyD88 is an essential adaptor protein in the signalling networks that are triggered by the binding of bacterial and viral components to Toll-Like Receptors or by the interaction of interleukins 1, 18 and 33 with their receptors.

Philip's talk, to an audience that mainly comprised patients with Waldenstrom’s lymphoma, their physicians, relatives and friends, focused on how MyD88 was discovered, and its key role in the innate immune system that is vital for protection against infection by microbial pathogens, especially during childhood. He also explained how the hyper-activation of the MyD88-dependent signalling network can lead to autoimmune diseases, such as lupus, and how its constitutive activation caused by the MyD88[Leu265Pro] mutation leads to lymphoma.

The talk was followed by a formal dinner in the Churchill rooms, at which Philip and Tricia Cohen were the guests of honour.




 

Most Cited paper
13 August, 2014
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Philip Cohen (L) and Kris Clark (R) with Biochemical Journal citation

The Biochemical Journal have announced that a paper published by Kris Clark in 2011, when he was a Postdoctoral Fellow in Philip Cohen's lab, is the most cited paper published in the Signal subsection of the journal over the two year period ending July 2013.

The paper, published in Biochem J. (2011) 434, 93-104 , describes the discovery of a novel feedback control pathway by which the IKK-related kinases, TBK1 and IKKepsilon, restrict the activation of the canonical IKK complex to prevent the overproduction of pro-inflammatory cytokines. Kris Clark subsequently found that this feedback control device is critical to prevent autoimmune disease: Clark et al, 2011, PNAS 108, 17093-17098.

For these and other discoveries Kris has previously received an Early Career Development Award from the Biochemical Society , and was recently awarded a Career Development Fellowship from Arthritis UK.




 

Orkney International Science Festival Gears Up For a Visit from The MRC-PPU
5 August, 2014
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Orkney International Science Festival

Dr. Howie Firth, Director of the Orkney International Science Festival (OISF) is in high spirits, planning for the upcoming Festival (September 4-10, 2014). He has a number of very diverse topics planned for talks and events, from physics and astronomy to marine biology, psychology and history. New for 2014, is biochemistry.

Dr. Firth invited Professor Karim Labib to the OISF to give a talk on the research he is pursuing at the MRC-PPU on DNA replication. In addition to this, Professor Labib will be meeting with senior secondary school students who are pursuing their Highers in biology and chemistry during his visit – to encourage the next generation of scientists.

In an effort to highlight the MRC-PPU to all of those planning their visit to Orkney, Mr. Firth spent part of June meeting with OISF visitors. Along with artist and videographer Ms. Selena Kuzman, they traversed Scotland and were gracious enough to stop in Dundee to meet with MRC-PPU Director, Professor Dario Alessi to learn more about the Unit’s efforts. A video interview and article contributed by Professor Alessi describing more about the PPU’s mission and efforts to make an impact on human disease were incorporated into Frontiers magazine, which highlights ongoing science in Orkney and beyond.

Scientists in Dundee are eager for future visits to Orkney to share their passion for biochemistry and all science and are hopeful that this is the beginning of a great partnership with the Festival in Orkney.

To learn more about the Orkney International Science Festival, please visit http://oisf.org/




 

Graeme Carnegie (1974-2014)
24 July, 2014
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Graeme Carnegie

It is with heavy hearts that we pass on the sad news that Dr Graeme Carnegie passed away peacefully on the 20th of July 2014, after a brave and prolonged battle with leukaemia. Graeme is remembered with huge affection and pride in Dundee, where he was a PhD student with Tricia Cohen from October 1997 to September 2001 and a friend and colleague to a generation of Dundee scientists and support staff.

Graeme's Ph.D. research focused on the role of the protein phosphatase 4 (Ppp4) in microtubule organisation at centrosomes and other cellular functions. He demonstrated that a regulatory subunit (R2) was likely to target the catalytic subunit to centrosomes in human cells and identified a R2 orthologue in the fruit fly. Graeme's investigations were the first to show that R2-Ppp4 interacts with a number of proteins, one of these being the Survival of Motor Neurons (SMN) protein complex, which is functionally defective in the hereditary disorder spinal muscular atrophy. The research provided the first information on how the SMN complex may be regulated during the assembly and recycling of spliceosomes and transcriptosomes. Graeme was awarded a conference poster prize for these studies.

Graeme’s postdoctoral research was carried out in the USA with John Scott, a Howard Hughes Investigator at the Vollum Institute in Portland, Oregon, where he published important research in the field of A-kinase anchoring protein-mediated signalling and demonstrated his ability to become an independent investigator. This led to his appointment as an Assistant Professor in the Department of Pharmacology at the University of Illinois at Chicago in 2010. Here he began his own research laboratory, focusing on the signalling complexes that may modulate the function of the heart in health and disease.

Graeme is fondly remembered by all his Dundee colleagues as a kind, thoughtful and talented scientist who epitomised the friendly, collaborative approach to research that most aim for but few reach. Indeed, his smile and superb sense of humour lit up any room he was present in, and his remarkable knowledge of music, film, literature and unusual alcoholic beverages enlivened every moment that his colleagues, including Pat and Claire Eyers, James Hastie, Mirela Delibegovic, Nimesh Mody and Mark Peggie were privileged to spend with him. They remember Graeme also as a gifted drummer and sportsman, equally at home on the football field, badminton or squash court, where his skills even extended to playing left handed ‘to make it a bit more of a game’. A man of integrity, generosity and wit, Graeme will be missed enormously by all his colleagues. Our heartfelt sympathy is extended to Graeme’s family in the UK and US, in particular his wife Andrea and his children Niamh and Ava.




 

MRC-PPU Clinical PhD Fellowship
17 July, 2014
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MRC-PPU Clinical PhD Fellowship

Two Clinical PhD Fellowships are available within the MRC Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU) in the fields of Cancer or Neurodegeneration

These Fellowships seek to provide state-of-the-art training in molecular research to ambitious medical graduates with an enthusiasm for biomedical research, seeking a career in academic medicine.

The MRC-PPU is a world-leading centre for understanding how defects in cell signalling pathways (with particular emphasis on protein phosphorylation and ubiquitylation) are linked to human disease. A key aim is to make research discoveries that stimulate new strategies to better diagnose and treat diseases in the future.

The Unit has 17 internationally recognised research groups involved in unraveling the molecular mechanisms underlying a range of important human diseases including cancer, inflammation, anaemias, hypertension and neurodegeneration. The Unit is based in the College of Life Sciences at the University of Dundee, one of Europe’s leading research institutes. It also has close links with Dundee Medical School and teaching hospitals.

We believe that we would be able to provide a fantastic environment to inspire and support talented and motivated medical graduates wishing to obtain training in fundamental research relevant to human disease.

In recent years the Unit has successfully trained clinicians undertaking Clinical PhD Fellowships and Clinician Scientist Fellowships. Dr Miratul Muqit, a Wellcome Trust Senior Clinical Fellow and Principal Investigator at the MRC-PPU, will play a key role in mentoring Clinical MRC-PPU Fellows.

We are also offering the possibility for potential candidates to undertake a 3-month trial research project in our Unit before embarking on a PhD.

Anyone interested can contact us at any time for further information. Please contact:

John Rouse (Director of MRC-PPU PhD Programme - j.rouse@dundee.ac.uk

Miratul Muqit (Wellcome Trust Senior Clinical Fellow & Honorary Consultant Neurologist - m.muqit@dundee.ac.uk

Dario Alessi (MRC-PPU Director) - d.r.alessi@dundee.ac.uk




 

Susan Taylor presents the Biochemical Society Centenary Award Lecture
17 July, 2014
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Susan Taylor and Ron Laskey

Susan Taylor from the Howard Hughes Medical Institute, University of California San Diego, USA,
presented the Biochemical Society Centenary Award Lecture at the College of Life Sciences on Monday, 14 July 2014.

Susan Taylor is a pioneer in the protein kinase research field and elected to deliver her Biochemical Society Centenary Award Lecture for her textbook work on defining the structure and mechanism by which the cyclic AMP dependent protein kinase PKA is regulated and functions in Dundee.

The body of work Susan Taylor has undertaken on the PKA system has made a tremendous contribution to the foundations of our current understanding of how protein kinases are regulated and function, and how disease-causing mutations impact on enzyme catalytic properties and hence disease. The knowledge derived from Susan Taylor’s work has contributed to the development of exquisitely specific and potent kinase inhibitors which over 20 have now been clinically approved drugs that are benefiting an ever increasing number of patients.

Susan’s talk was entitled “PKA: Dynamic Assembly of Alloseteric Macromolecular Signaling Complexes"

Professor Ron Laskey FRS CBE, President of the Biochemical Society, presented Susan with her award.




 

Short film featuring the Rouse Lab Helps Promote Cancer Research
11 July, 2014

The Rouse lab featured recently in a video to help the local charity Worldwide Cancer Research, with the idea of explaining to potential donors how scientific research works and to outline what it is that scientists actually do on a day-to-day basis.

Worldwide Cancer Research (formerly known as the Association for International Research – AICR) is based in St. Andrews. As well as providing a limited number of fellowships for new group leaders, the charity provides project grants – small grants which typically fund a student or postdoc for 2-3 years – to groups all over Europe. These days WCR can only fund around 7% of the project grant applications it receives because of a major increase over the past few years in the number of applications. To allow many more grants to be funded, a major fundraising effort has been launched. The promotional video featuring the Rouse lab, which can be found at the link below, will be used as part of that effort. The idea for the film happened when three research scientists from Dundee in receipt of WCR funding (John Rouse, Paul Clarke and Gareth Inman) hosted an open day for the entire staff of WCR and the Board of Trustees, to talk about future directions in cancer research.

Click here to see the film.




 

Research reveals how the canonical IKK complex is activated
10 July, 2014

New research has uncovered how a complex protein pivotal in the development of viral infection and autoimmune diseases is activated. The discovery answers a key question about one of the most widely-researched proteins in human biology, which has been the subject of tens of thousands of research papers.

Jiazhen Zhang, a research student in Philip Cohen’s laboratory, uncovered how the canonical IκB kinase is activated. The results are published today in the Biochemical Journal.

NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) is a protein complex that controls transcription of DNA. NF-κB plays a key role in regulating the immune response to infection. Incorrect regulation of NF-κB has been linked to inflammatory, and autoimmune diseases, septic shock, viral infection.

“NF-κB has been the subject of a vast amount of research for many years as it plays a critical role in inflammatory diseases and cancer,” said Sir Philip. “It has been known for some time that the protein is activated by a kinase called IKKβ but there has been split opinion with regards to how the kinase itself is switched on.

“We have confirmed that another kinase, TAK1, is involved, but surprisingly it isn’t sufficient to switch on IKKβ. Two other events need to happen in addition, namely the formation of a hybrid ubiquitin chain and its attachment to the NEMO regulatory component of the canonical IKK complex as we showed in a paper last year (Emmerich (2013) PNAS, 110, 15247) and then the addition of a second phosphate group on to IKKβ which remarkably is carried out by IKK itself. It is only then that IKKβ becomes competent to switch on NF-κB.

“This is complex biochemistry but working out the details of how proteins are switched on and off is how new ways to develop improved drugs to treat disease are identified. For example, the enzyme that makes the ubiquitin chains needed to activate IKKβ could now be targeted to develop a drug to treat inflammatory diseases.”

Peter Shepherd, Chair of the Biochemical Journal Editorial Board, said, “This signalling pathway is critical for a wide range of cellular responses, particularly stress responses. Understanding how this pathway is regulated is hugely important, and this paper finally clarifies one of the key steps in this process. This is important in not only understanding the disease process, but in the quest to develop new therapies that target this signalling pathway.”




 

Esther Sammler awarded Starter Grant for Clinical Lecturers
4 July, 2014
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Dr Esther Sammler

Congratulations to Esther Sammler who has been awarded a highly prestigious £30,000 starter grant for clinical lecturers by the

Academy of Medical Sciences. The scheme funds outstanding, research active, clinical lecturers to pursue their research interests and strengthen their future career aspirations.

Esther only recently completed her PhD degree in the lab of Dario Alessi on the "Signalling pathway of FBXO7 and its role in hereditary Parkinsonism" as a Wellcome Trust Clinical PhD student. She is now back to treating patients with Parkinson's disease and other neurological conditions as a clinical lecturer in the neurology department in Ninewells Hospital and Medical School, but continues to work on her exciting FBXO7 project in the MRC-PPU.

Esther's clinical and research interests focus on neurodegenerative diseases and neurogenetics; the driving force behind her academic work is the explicit lack of effective treatments for patients with such conditions.

Esther commented "I am delighted and very grateful to the Academy of Medical Sciences for their generous support of my work. I would also like to thank the Anonymous Trust who in May this year also awarded me £10,000 to support my research. Their generous support will help me to complete final aspects of my PhD project, and I am already starting to think about future directions."




 

Agne Kazlauskaite selected to attend Roche Continents 2014
25 June, 2014
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Agne working in the lab

Agne Kazlauskaite, a PhD student in the MRC Protein Phosphorylation and Ubiquitylation Unit, has been selected to attend the prestigious Roche Continents programme that will take place in Salzburg, Austria this summer.

The Roche programme brings together 100 of the most creative students in science, music and art from all over Europe to participate in a series of seminars, workshops, and concerts taking place in in Salzburg, during the world-famous Salzburg music festival.

Agne, who is currently in the 3rd year of her PhD, has been working between the labs of Dario Alessi and Miratul Muqit and has made groundbreaking progress in the understanding of two enzymes, PINK1 and Parkin, that are mutated in familial Parkinson’s disease. Most recently Agne discovered that PINK1 can directly phosphorylate ubiquitin at Serine65 and that this modified form of ubiquitin can activate Parkin ubiquitin ligase activity. Her work has shed considerable molecular insight into this progressive disorder and stimulated new ideas on how it could be treated with drugs.

On hearing of her success at obtaining a place at Roche Continents, Agne said “I'm thrilled to have the opportunity to attend such an exciting conference and to expand my horizons by meeting people from such a wide range of backgrounds. I hope it will inspire me with new ideas for my future work!”




 

Philip Cohen awarded Albert Einstein Prize by the World Cultural Council
10 June, 2014

Philip Cohen, a Programme Leader in the MRC Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), has been awarded the 2014 ALBERT EINSTEIN World Award of Science from the World Cultural Council, which he will receive on November 17th 2014 at a ceremony to be held at Aalto University Finland. The award was made by the World Cultural Council’s Interdisciplinary Committee including eminent scientists from all five continents.

The prize, which consists of a diploma, and commemorative medal and cheque for ten thousand US dollars, has been awarded for “his 40-year outstanding and continuing scientific career devoted to studying and establishing the profound importance of protein phosphorylation in regulating almost every physiological process. Professor Cohen's achievements meet the criteria for the ALBERT EINSTEIN World Award of Science most closely in respect to bringing "true benefit and well-being to mankind" in their importance to the development of drugs and treatment with global impact. Professor Cohen’s pivotal contribution has been to elucidate a major section of the insulin signal transduction-signalling pathway, essentially from scratch, starting at a time when virtually nothing was known about cell signalling. This was to be based on his dissection of protein kinase dependent cascades, which are the major intracellular components of hormonal signalling networks. His research has raised Dundee University to one of the leading academic institutions in his field of this study. Professor Cohen has made decisive contributions to the growth and international reputation of life sciences at the university and to the development of a life sciences cluster in the city, which now accounts for 16% of its economy. In fact, the College of Life Sciences has, for several years, been voted one of the best scientific environments in the world in which to work. Throughout his career Philip Cohen has been an exceptional mentor of talented young researchers. More than one hundred PhD students and postdoctoral scientists have trained in his laboratory over thirty-eight years, with the vast majority now working in senior roles as academic research leaders.”
To read the full citation click here.

Commenting on the award Philip said:
“This award has come completely out of the blue as I had no idea that I had even been nominated.” It is a great honour not just for myself and my family, but also for the MRC-PPU, the College of Life Sciences at the University of Dundee and the 100 plus students and postdocs who have underpinned the success of my laboratory over the past 43 years.”

Immediately after the award ceremony finishes, Philip will fly from Helsinki to China where he will give a lecture at a conference to mark the founding of the Shanghai Institute for Advanced Immunochemical Studies. The organisers of the Shanghai conference have kindly agreed to reschedule his talk to enable him to attend both events.




 

Sapkota lab publishes paper describing role of deubiquitylating enzyme USP15 on bone morphogenetic protein (BMP) signalling
21 May, 2014

Congratulations to Lina Herhaus and Mazin Al-Salihi, of Gopal Sapkota's lab, for publishing a paper in Open Biology that describes how USP15 regulates the BMP pathway by deubiquitylating the type I BMP receptor, ALK3.

BMPs belong to the transforming growth factor β (TGFβ) family of cytokines and play fundamental roles in development and tissue homeostasis. BMPs control many cellular processes, including proliferation, differentiation and morphogenesis. Therefore, abnormal BMP signalling is associated with several human diseases, including bone defects and cancer. Protein kinase ALK3 mediates BMP signalling through phosphorylation and activation of SMADs 1/5/8. SMAD6, a transcriptional target of BMP, negatively regulates the BMP pathway by recruiting E3 ubiquitin ligases and targeting ALK3 for ubiquitin-mediated degradation. This paper describes the identification of the deubiquitylating enzyme USP15 as an interactor of SMAD6 and ALK3 and a regulator of BMP signalling. USP15 enhances BMP-induced phosphorylation of SMAD1 by interacting with and deubiquitylating ALK3, while mitigating the inhibition of BMP signalling caused by SMAD6. Consequently, the depletion of USP15 increases ALK3 K48-linked polyubiquitylation, and inhibits both BMP-induced SMAD1 phosphorylation and transcription of BMP target genes. Furthermore, loss of USP15 expression from mouse myoblast cells inhibits BMP-induced osteoblast differentiation.

Consistent with the findings in human and mouse cells (mostly Lina’s and Mazin’s efforts), Kevin Dingwell (Jim Smith’s laboratory at NIMR, London) demonstrated that xUSP15 also modulates BMP-induced phosphorylation of SMAD1 and transcription during Xenopus embryogenesis.

This paper was a mammoth effort by everyone in Gopal’s lab, with contributions made also by Tim Cummins, Janis Vogt, Lize Wasmus and David Bruce. Richard Ewan, Thomas Macartney and Simone Weidlich also contributed to the paper. Collaborators Kevin Dingwell and Jim Smith (NIMR, London) contributed substantially to this work.

The paper entitled “USP15 targets ALK3/BMPR1A for deubiquitylation to enhance bone morphogenetic protein signalling” is available via Open Biology.




 

MRC-PPU researchers run Monikie 10k
13 May, 2014
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MRC-PPU runners at Monikie

Several MRC-PPU researchers took part in this weekend's Monikie 10k run

Results from left to right were:

Sambit Nanda 01:12:13
Jiazhen ‘Roy’ Zhang 00:50:05
Catherine Rodger 00:55:47
Sam Strickson 00:48:12
Stefan Vollmer 00:54:39
Alberto Moreno (GRE) 00:50:07
Dario Alessi 00:52:49
Laia Pedro-Roig 00:58:53
Juanma Ortiz-Guerrero 00:52:45
Meghan Slean 00:54:19
Ivan Munoz 00:44:13
Max Fritsch 00:50:12

Congratulations to Ivan for being the fastest researcher in the unit!




 

The International Centre for Kinase Profiling Website Undergoes a Facelift
12 May, 2014

A quick google search for ‘kinase profiling’ yields the International Centre for Kinase Profiling (ICKP), housed in the MRC-PPU as the top-hit. Established as a service in 1998, the ICKP works with academic labs, biotechnology and pharmaceutical companies to provide a reliable, rapid and cost-effective means to interrogate a customer’s compound of interest against a broad panel of protein and lipid kinases.

Kinases are the pharmaceutical industry’s most important class of drug target, yet one of the primary challenges is to develop a drug that selectively suppresses the activity of one, or at most a few, of the 500 protein kinases encoded by the human genome. As the MRC-PPU is home to the world’s leading experts on kinases and phosphorylation, evolution of the ICKP was a natural one.

The recent face-lift of the website, though seemingly cosmetic, goes more than skin-deep. It was focused on streamlining access to the critical information about the ICKP’s services and expertise more readily. The hope is that this will in turn ensure that scientists world-wide can interrogate their compound of interest more quickly, thereby accelerating their research.

The ICKP has always offered several ranges of kinase screens (Premier, Express, and Lipid) and has added a ‘Custom’ screen to assist researchers to better tailor their screen. In addition to these services, staff at the ICKP can assist with IC50 determination, ATP Competition Assays, and Substrate Screens.

To visit the International Centre for Kinase Profiling website and identify the service that best suits your research please visit http://www.kinase-screen.mrc.ac.uk/ and please do spread the word to your colleagues and collaborators.

ICKP staff welcome your comments and suggestions on how to improve the site further. Please send all of your suggestions, no matter how minor, to kinase-screen@dundee.ac.uk




 

Sourav Banerjee's research uncovers remarkable interplay between NUAK1 and PLK1 kinases
7 May, 2014
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NUAK1

Much research in the MRC-PPU has focused on understanding the regulation and function of two related protein kinases termed NUAK1 and NUAK2 that are activated by the LKB1 tumor suppressor. LKB1 phosphorylates these enzymes at their T-loop residues stimulating their activity. Little is known about the NUAK enzymes, although some initial work indicates that they are likely to play diverse roles including controlling cell survival, senescence, adhesion and polarity.

Only a single substrate, namely the MYPT1 subunit of the PP1βMYPT1 myosin phosphatase complex, has been reported. This finding was made by Anna Zagorska who previously undertook her PhD in the Alessi lab in the MRC-PPU. Anna’s data suggested that NUAK1 phosphorylation of PP1βMYPT1 triggered binding to 14-3-3 isoforms and lead to an inhibition of phosphatase activity.

Previous work by other groups has also revealed that PP1βMYPT1 acts to inactivate PLK1 by dephosphorylating the T-loop Thr210 residue, thereby controlling mitosis. The ability of PLK1 to interact with PP1βMYPT1 is dependent upon phosphorylation of MYPT1 at Ser473 by the cyclin dependent protein kinase-2 (CDK2), which creates a docking site recognised by the Polo-box domain of PLK1. Interestingly, Ser473 lies immediately adjacent to the NUAK1 phosphorylation site (Ser472) that controls 14-3-3 binding. This therefore suggests that phosphorylation of MYPT1 by NUAK1 and 14-3-3 binding could directly interfere with the ability of PP1βMYPT1 to interact with and hence dephosphorylate PLK1.

Intrigued by all of this, a PhD Student in Alessi lab, Sourav Banerjee, has spent the last few years exploring links between NUAK1 and components that regulate cell cycle and PLK1. This research has lead Sourav to discover that expression of NUAK1 is controlled by cyclin dependent kinase (CDK), Polo kinase (PLK) and the Skp, Cullin, F-boxβTrCP (SCFβTrCP) E3 ubiquitin ligase complex. His findings indicate that CDK phosphorylates NUAK1 at Ser445, triggering binding to PLK. PLK1 then subsequently phosphorylates NUAK1 at two conserved non-catalytic Ser residues (Ser476 and Ser480). This induces binding of NUAK1 to βTrCP, the substrate recognition subunit of the SCFβTrCP E3 ligase, resulting in NUAK1 becoming ubiquitylated and degraded.

Sourav also found that NUAK1 and PLK1 are reciprocally controlled in the cell cycle. In G2-M phase when PLK1 is most active, NUAK1 levels are low and vice versa in S-phase when PLK1 activity is low, NUAK1 is more highly expressed. Moreover, Sourav found that NUAK1 inhibitors (WZ4003 or HTH-01-015) suppresses proliferation by reducing the population of cells in S-phase and mitosis an effect that can be rescued by overexpression of a NUAK1 mutant in which the Ser476 and Ser480 residues are mutated to Ala to prevent ubiquitylation by SCFβTrCP.

Sourav also showed that consistent with a role of NUAK1 inhibiting PP1βMYPT1 and PP1βMYPT1 acting on PLK1, that subjecting cells to a treatment that induces them to detach from the matrix that they are growing on, which results in a marked phosphorylation and inhibition of PP1βMYPT1 by NUAK1, resulted in a significantly enhanced the T-loop phosphorylation of PLK1 at Thr210. This phosphorylation of the Thr210 induced by NUAK1 phosphorylation of MYPT1-is accompanied by an electrophoretic band-shift of PLK1 indicating that the stoichiometry of phosphorylation is significant. Importantly, this effect on PLK1 Thr210 phosphorylation following cell detachment was prevented by the NUAK1 selective WZ4003 inhibitor.

Sourav’s work provides further insights into the biological regulation of the NUAK isoforms and highlights the remarkable interplay that exists between CDKs, Polo kinase, NUAK1, PP1βMYPT1 and SCFβTrCP signalling components (see Figure). To read a copy of Sourav’s paper click here.

Sourav is now departing the MRC-PPU to start a postdoc in Jack Dixon's laboratory in San Diego and we wish him all the best for the future.




 

Superhero science at Forthill Primary School
25 April, 2014

Scientists and support staff from the MRC PPU recently enjoyed a visit with a P3 class at Forthill Primary for a fun morning of hands on experiments with a Superhero theme.

Laura Grasso demonstrated Wolverine’s fast healing abilities through the explanation of blood components using sunflower oil and sweets, which proved to be too much of a temptation for some of the kids. Dry ice bubble experiments were lead by Laurel Chandler linking to Elsa from Frozen’s special cold powers. Magneto’s powers, along with homemade compasses, were both explained by Elaine Forsyth through the use of magnets, with one boy commenting "so when the magnets are attracted to each other that’s like when you fancy someone?" Finally, the kids were encouraged to copy Superman’s super breath, using a simple lung function test, by Gail Gilmour. The morning was rounded off outside with a few messy Pepsi and Mentoes explosions, which the children (and admittedly the adults!) found extremely funny using homemade triggers to obtain the highest geysers.

Overall, the morning proved to be a big hit and provided a fun introduction to hands-on general science experiments for the P3 children. There was plenty of loud vocal appreciation from the children and assurances from many that scientist is now their primary career choice.




 

Kris Clark awarded prestigious Arthritis Research UK career development fellowship
16 April, 2014
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Kris Clark

Dr Kris Clark has been awarded a prestigious fellowship from Arthritis Research UK that will support his groundbreaking work developing new treatments for inflammatory arthritis over the next five years. As a result of this he has been awarded an Independent Investigator position within the MRC-PPU.

The career development fellowship provides £400,000 of funding which will allow Dr Clark to establish his first independent laboratory within the MRC Protein Phosphorylation and Ubiquitylation Unit in the College of Life Sciences at Dundee.

Dr Clark’s research focuses on the signaling pathways controlling the resolution of inflammation. Inflammatory arthritis, of which rheumatoid arthritis is the most common form, is a serious auto-immune condition leading to painful, swollen joints, affecting one per cent of adults.

As a senior postdoctoral researcher in Philip Cohen's lab, Dr Clark discovered two novel mechanisms that limit the inflammatory response, for which he received an Early Career Research Award from the Biochemical Society in 2013.

Most recently he made a major breakthrough by identifying a key role for the SIK sub-family of protein kinases in helping control inflammation, and it is this aspect of his research that Dr Clark will focus on as an Independent Investigator.

“I am very grateful to Arthritis Research UK for providing the funding necessary to establish my own research team in Dundee,” said Dr Clark. “The generous funding will allow my group to tackle the challenge of identifying new therapeutic approaches for the treatment of rheumatoid arthritis.

“Most current therapies block the actions of toxic, pro-inflammatory molecules, but drugs that also enhance the production of beneficial anti-inflammatory molecules to stop inflammation and repair the damaged tissue could have important advantages over current treatments.”

Dr Clark’s lab will aim to understand how the function of cells of our immune system called macrophages is controlled in the body and how developing drugs that interfere with these processes could be used to treat rheumatoid arthritis and related human diseases.

The research programme is based on his recent discovery that drug-like molecules that block enzymes called SIKs generate a macrophage population that stops inflammation and drives tissue repair.

Dr Clark will now set out to establish how the SIKs control macrophage behavior and, in collaboration with Professor Iain McInnes at the University of Glasgow, evaluate whether drugs that switch off these enzymes are likely to improve the treatment of rheumatoid arthritis.

Professor Dario Alessi, Director of the MRC Protein Phosphorylation and Ubiquitylation Unit, commented, "This is a tremendous accolade for Kris. The award of this highly sought after fellowship will enable Kris to develop his research into uncovering the roles that the SIK enzymes play in mediating autoimmune conditions such as rheumatoid arthritis.

“This research is vital, as Kris’s data indicates that if drugs could be developed that acted on SIKs, this could lead to new improved treatments for autoimmune conditions. One of the main goals of Kris’s work will be to work with pharmaceutical companies to try to generate new autoimmune therapies by developing drugs that act on SIKs.”

Dr Clark was born and raised in Montreal, Canada where he obtained a BSc in Biochemistry from Concordia University. After carrying out several short research projects in Canada, Australia and the Netherlands, Dr Clark worked on the mechanisms that regulate the adhesion of cancer cells at Radboud University Nijmegen, the Netherlands for which he received his PhD degree in 2007.

During his PhD, Dr Clark obtained a FEBS Short-Term Fellowship to visit the MRC Protein Phosphorylation Unit in March 2006 to map phosphorylation sites on the proteins he was studying. This visit inspired him to refocus his research to investigate the role of protein phosphorylation in innate immunity. He therefore returned to the MRC-PPU in May 2007 to join Philip Cohen’s lab after winning a Long-Term Fellowship from the European Molecular Biology Organization.

To learn more about Kris’s research programme see here.




 

Philip Cohen elected Corresponding Member of the Australian Academy of Science
10 April, 2014

Philip Cohen has been elected a Corresponding Member of the Australian Academy of Science, one of only 27 scientists from around the world to hold the honour.

Philip was recognised for his outstanding contributions to the life sciences. The list includes two Nobel Laureates, while Sir David Attenborough is one of the eight Corresponding Members from the UK.

“I was greatly surprised and honoured to learn that I had been elected a Corresponding Member of the Australian Academy of Science as it is a rather exclusive club” said Sir Philip.

Philip’s contributions to science in Australia were made during a number of visits to the country starting in 1980. He has given lectures at conferences and at every major university in Australia as well as public lectures in Melbourne, Victoria and Newcastle, where he talked about how Life Sciences and Biotechnology transformed Dundee. His research has influenced the work of countless Australian researchers, and his laboratory in Dundee has hosted a number of visiting professors from Australia who have gone on to make their mark on the scientific community.




 

Agne Kazlauskaite defines PINK1 as the first ubiquitin kinase
26 March, 2014
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Agne Kazlauskaite

Exactly 10 years ago mutations in a little studied kinase called PTEN-induced kinase 1 (PINK1) were discovered in patients with early-onset Parkinson’s disease [Ref 1]. PINK1 is unique amongst all kinases in possessing a N-terminal targeting domain that localizes it to the mitochondria. There has been great interest in understanding the function of PINK1 however, the human enzyme was difficult to express and exhibited very low levels of kinase activity, which hampered early progress.

In 2011, PhD student, Helen Woodroof, (supervised by Miratul Muqit, Daan van Aalten and Dario Alessi) made a breakthrough by discovering constitutively active insect orthologues of PINK1, which led to the establishment of the first assays of PINK1 kinase activity in the field [Ref 2]. Another PhD student, Chandana Kondapalli (supervised by Miratul Muqit and Dario Alessi) then deployed insect PINK1 in a screen to identify the Parkinson’s linked ubiquitin E3 ligase, Parkin as the first PINK1 substrate. Chandana mapped the phosphorylation site to Serine65 (Ser65) that lies within the N-terminal Ubiquitin-like (Ubl) domain of Parkin [Ref 3]. She also raised a phospho-specific antibody to demonstrate that the Parkin Ser65 site was phosphorylated by PINK1 in cells in vivo.

Parkin is a RING-IBR-RING E3 ubiquitin ligase and mutations had been discovered in Parkinson’s patients in 1998. For many years it was believed that Parkin was constitutively active. However, Helen Walden whilst at the CRUK laboratories in Lincolns Inn Fields, made a major advance by discovering that Parkin is autoinhibited and showed that this was mediated by its Ubl domain [Ref 4]. However, the physiological signal to convert Parkin from an inactive to active conformation was unknown. Agne Kazlauskaite, a PhD student (supervised by Dario Alessi and Miratul Muqit) set out to test whether PINK1-dependent phosphorylation of Parkin at Ser65 could be that signal and in a series of experiments published in two papers demonstrated that Parkin Ser65 phosphorylation indeed was critical for Parkin activation as judged by monitoring the ubiquitylation of the Parkin substrate Miro1 as well as Parkin autoubiquitylation and the formation of free polyubiquitin chains [Ref 3 and Ref 5].

However, an outstanding question was how PINK1-dependent phosphorylation of Parkin at Ser65 led to activation of its ubiquitin E3 ligase activity. The answer came unexpectedly when Chandana Kondapalli working with Matthias Trost’s lab undertook a phosphoproteomic screen to identify novel PINK1 substrates. Strikingly they identified a novel ubiquitin phosphopeptide phosphorylated at Ser65 that was significantly enriched in cells over-expressing wild-type PINK1 activated by the mitochondrial-uncoupling agent, CCCP, compared to cells expressing kinase-inactive PINK1. Ser65 in ubiquitin lies in a similar motif to Ser65 in Parkin’s Ubl domain.

Agne Kazlauskaite next investigated the functional role of ubiquitin Ser65 phosphorylation. Remarkably Agne found that PINK1 could directly phosphorylate ubiquitin at Ser65. In a series of experiments she next demonstrated that Ser65-phosphorylated ubiquitin (ubiquitinPhospho-Ser65) was an activator of Parkin. She initially demonstrated that wild-type but not kinase-inactive PINK1 could still activate a fragment of Parkin that lacks the Ubl domain (encompassing the Ser65 residue) (Ubl-Parkin). Axel Knebel’s lab then expressed and purified ubiquitinPhospho-Ser65 and the isolated Parkin Ubl domain phosphorylated at Ser65 (UblPhospho-Ser65). Agne was able to show that ubiquitinPhospho-Ser65 but not non-phosphorylated ubiquitin could activate Ubl-deleted Parkin. She also found that UblPhospho-Ser65 could also activate this Ubl-deleted Parkin similar to ubiquitinPhospho-Ser65. Interestingly Agne found that ubiquitinPhospho-Ser65 could activate full-length Parkin but this was not the case for non-phosphorylated ubiquitin or UblPhospho-Ser65. Finally Agne was able to show that both PINK1-dependent phosphorylation of Parkin at Ser65 as well as ubiquitin at Ser65 is required for optimal activation of Parkin E3 ligase activity since only mutation of both proteins at Ser65 leads to complete loss of Parkin E3 ligase activity.

Agne’s new findings suggest that small molecule activators of Parkin that mimic ubiquitinPhospho-Ser65 could represent a promising therapy for Parkinson’s. Her work also provides the most stark example to date of the convergence of protein phosphorylation with protein ubiquitylation and opens a new area of research in determining the role of phospho-ubiquitin in Parkinson’s disease and beyond.

To read a copy of Agne’s paper published in Biochemical Journal click here




 

Axel Knebel receives CLS Innovator of the Year Award for developing a new protein affinity purification tag
24 March, 2014
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Axel Knebel

Many congratulation to Axel Knebel who has just received the CLS Innovator of the Year Prize for the development of a novel affinity purification tag termed the “Dac-tag”.

Axel, runs the MRC-PPU Protein Production and Assay Development in the ubiquitylation system team that generate the majority of ubiquitylation reagents that the MRC-PPU researchers and their collaborators depend on.

Axel developed the Dac-tag in order to greatly facilitate the purification of recombinant proteins from bacteria or insect cells. Using this methodology Axel and his team have been able to obtain incredibly pure preparations of enzymes especially from insect cell expression systems to a much greater degree than could be achieved with other tags such as His, maltose binding and GST. The Dac-tag is now becoming the frontline choice for the affinity purification of recombinant proteins from insect cells. It also has benefits as it is a monomeric and highly soluble protein that helps stabilise and enable better expression of recombinant proteins.

The Dac-tag is based on a fragment of penicillin binding protein 5 (PBP5 residues 37-297), which binds in a pseudo reversible manner to ampicillin Sepharose. In order to obtain a pure protein of interest, the Dag-tag is cloned to the N or C-terminal end of the protein. Because of the properties of the Dac-tag, this fusion protein can then be readily isolated in a highly purified manner using ampicillin Sepharose, which is very selective for penicillin binding proteins. The Dac-tag has the advantage that it is monomeric and does not rely on cysteine chemistry or metal affinity, so it is ideal for purification of proteins in the Ubiquitin arena. Ampicillin or amoxycillin, coupled to NHS-activated Sepharose provide high capacity. Any protein fused to the PBP5 residues 37-297 will rapidly bind to such a Sepharose and can be eluted in a buffer system containing 10mM ampicillin and 5% glycerol. Without these eluents the tag binds tightly and a protein can be recovered for example by using a protease site between the tag and the target protein.

To read the paper describing the development and use of the Dac Tag click here. Examples of the proteins that Axel has purified using this system include the Cullin-1 CDC53/Hrt1 complex, the Cul5/RNF7 and APPBP1/UBA3 complexes as well as the Cullin3-SKP1-KLHL3 complex that plays a critical role in regulating human blood pressure.

The Dac-tag is now being marketed by Expedeon Ltd under the name ‘Cool-tag’. Axel Knebel stated "I am very pleased to receive CLS Innovator of the Year Award for developing a the Dac-tag. I hope that it will help researchers to more easily isolate highly purified recombinant proteins and make a significant contribution to Medical Research. I am delighted to see this tag being widely utilised within the MRC-PPU and hope that its use will be quickly adopted by other researchers”.

Axel is the second MRC-PPU researcher to be awarded the CLS Innovator award the first being Ayaz Najafov a PhD student at the time in Dario Alessi's lab who developed the Protein Guru programme to help analyse mass spectrometry data.




 

Scientists from the University of Dundee Visit Newport Primary School
21 March, 2014

Recently, Newport primary school hosted a science week for its pupils (March 17th to the 21st). The pupils learned from a diverse team of experts representing many of the Centres at The University of Dundee including the MRC Protein Phosphorylation & Ubiquitylation Unit (MRC-PPU), The Centre for Dermatology and Genetic Medicine (DGEM) and College of Life Sciences (CLS). Leading the effort during this week were Deena Leslie Pedrioli (DGEM), Patrick Pedrioli (MRC-PPU), and Thimo Kurz (MRC-PPU) who were joined by several like-minded and equally enthusiastic PhD students and postdoctoral fellows: Vikas Hegde, Dun Jack Fu, Louise Stanley, Kamila Chughtai, Stella Ritorto, Kshitiz Tyagi, Van Kelly, Craig MacKay, Anna Kelner, Katharina Schleicher, and Erin Hardee. Together, they exposed pupils to a number of activities that enabled the children to experience first-hand what it is like to work in a biology lab. These included peering through the lens of a microscope in an effort to visualize the world beyond the naked eye and exploring the world of microbes around them by culturing microbes from both their handprints and objects around their classroom. Students also expanded their understanding of the biology of cells, and ultimately tissues, by building different cells out of Play-Doh. A picture is worth a thousand words and as one can see, the event was a hit, attended by over 200 students. The scientific team received many interesting questions and insightful observations during their visit. One particular interaction occurred after Dr. Pedrioli explained disease-causing mutation when a young student very astutely commented "So the cell is like a city and sometimes somebody breaks the law!" Ultimately, the pupils had a wonderful time and The University of Dundee may well expect to have some burgeoning young local scientists gracing their labs in a few years’ time!




 

Agne discovers first substrate to be regulated by PINK1-dependent phosphorylation of Parkin at Serine65
20 March, 2014
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Agne Kazlauskaite

Mutations in the PINK1 and Parkin genes are associated with early-onset Parkinson’s disease. PINK1 encodes a mitochondrial-localised protein kinase whilst Parkin encodes a RING-IBR-RING E3 ubiquitin ligase. In 2012 a former PhD student of Miratul Muqit and Dario Alessi, Chandana Kondapalli, discovered that PINK1 can phosphorylate Parkin at Serine65 (Ser65), a highly conserved residue that lies within the N-terminal Ubl domain of Parkin. Furthermore, current PhD student, Agne Kazlauskaite, supervised by Dario and co-supervised by Miratul, had demonstrated that phosphorylation of Parkin at Ser65 led to activation of its E3 ligase activity as determined using a substrate-free autoubiquitylation assay.

An outstanding question that Agne wished to address was whether Ser65 phosphorylation of Parkin was critical for its ability to ubiquitylate substrates. Several lines of evidence indicated that physiological substrates of Parkin may reside in the mitochondria and Miro1, an atypical mitochondrial GTPase, has recently emerged as a candidate substrate for Parkin.

Agne developed a novel assay of E3 ligase activity using full-length untagged Parkin and Miro1 and was able to demonstrate that Parkin could efficiently ubiquitylate Miro1 only upon phosphorylation by wild-type PINK1. Importantly she showed that Miro1 ubiquitylation was abolished using kinase-inactive PINK1 or a non-phosphorylatable Ser65Ala point of mutant of Parkin. Furthermore, in collaboration with Van Kelly, a PhD student in Patrick Pedrioli’s lab, she was able to map the sites of Miro1 ubiquitylation to highly conserved lysine residues, 153, 230, 235, 330 and 572. Agne next developed an E2-ubiquitin discharge assay to assess Parkin activity and found that Parkin could stimulate robust discharge of ubiquitin-loaded E2 only after phosphorylation of Parkin by wild-type PINK1 and not by the Ser65Ala Parkin mutant. Agne next deployed her assays to investigate the effect of Parkinson’s disease-associated point mutants of Parkin. Her analysis revealed that the majority of mutants tested led to disruption of Parkin E3 ligase activity including the catalytic cysteine mutant, Cys431Phe. However, Agne also identified mutants that increased Parkin E3 ligase activity as well as mutants that did not significantly alter activity.

Agne’s studies suggest that phosphorylation of Parkin at Ser65 is critical for its activation. The assays she has developed will be important to uncover new insights into Parkin biology as well as aid in the development of screens to identify Parkin activators that may have therapeutic potential in Parkinson’s.

To read a copy of Agne’s paper published in Open Biology, click here




 

Ex-MRC-PPU postdoc appointed Group Leader at University of Glasgow
20 March, 2014
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Xu Huang

Congratulations to Xu Huang who worked as a postdoc in Dario Alessi’s lab (November 2004-May 2008) who has just been appointed to a group leader position at The Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Research, University of Glasgow.

Whilst a postdoc in Dundee, Xu conducted important research that demonstrated that activating AMPK kinase in PTEN-deficient mice delayed the onset of tumour formation. The Biochemical Journal paper describing these findings currently has 148 citations. These findings also played an important role in stimulating many of the 196 different clinical trials that are taking place to evaluate the benefits of Metformin in preventing and treating human cancers. Xu also played an important role in the identification of the novel mTOR complex-2 component termed PROTOR, a paper that has 146 citations to date.

After training at the MRC-PPU Xu undertook a second postdoc with Dr Tim Somervaille, at the Paterson Institute for Cancer Research at The University of Manchester where he published interesting papers on the molecular basis of Leukaemia, identifying and validating a few potential candidates as therapeutic treatment targets in Acute Myeloid Leukaemia (AML).

In his future research Xu plans to combine his past and current experiences in cell signalling and epigenetic regulation in leukaemia cancer stem cells, exploring the potential cross-talk between them, and continue to identify novel pathways and targets in leukaemia, and says "I am looking forward to working with other group leaders in the Paul O'Gorman Leukaemia Research Centre, lead by Professor Tessa Holyoake, and I hope to be able to establish future collaborations with Dario and other former colleagues in Dundee."

We wish Xu every success in starting up his new research laboratory.




 

Helen Walden awarded Colworth Medal
13 March, 2014
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Helen Walden

Many congratulations to MRC-PPU PI Helen Walden who has been awarded the prestigious Colworth Medal.

The Colworth Medal is sponsored by Unilever and presented by the Biochemical Society, and is the most distinguished award that a biochemical researcher in the early stages of their independent research can receive in the UK. In addition to the medal, Helen will receive an honorarium of £3,000 and an invitation to present two lectures, one at a Biochemical Society meeting and another at the Unilever research laboratory.

Helen’s research focuses on understanding the fundamentals of the ubiquitylation system and how it is linked to disease mechanisms. Helen has made a series of wonderful discoveries that have resulted in a much better understanding of three important areas of the ubiquitylation system namely the E1 activating enzyme, and the E3 ubiquitin ligases, FANCL and Parkin. As a result of this work Helen has been able to establish a growing international reputation as a leader in the ubiquitylation area and published numerous highly cited research papers. In 2012 Helen also received an esteemed and highly sought after Young Investigator Award from the European Molecular Biology Organisation (EMBO).

Helen did her undergraduate training at the University of Bath before moving to St Andrews to perform her PhD with Professor Garry Taylor, where she worked on unravelling the structural basis of protein thermo-stability through X-ray analysis of thermostable proteins. Helen next undertook a postdoc, in the laboratory of Brenda Schulman at the St Jude Children’s hospital in Memphis (Dr Schulman’s first postdoc), to work on the ubiquitylation system. During this period Helen solved the first structure of an E1 activating enzyme, namely the heterodimeric E1 enzyme (APPBP1-UBA3). E1 enzymes play an important role in regulating ubiquitylation as they catalyse the first step in the ubiquitylation pathway. The dramatic structure and the analysis that Helen revealed the catalytic mechanism by which E1 functions.

In 2005 Helen then set up her own research group at the Cancer Research UK London Research Institute at Lincoln’s Inn fields. Here, Helen focused mainly on understanding two important E3 ligases namely Parkin and FANCL, biologically important enzymes that are mutated in patients with Parkinson’s disease and Fanconi Anemia respectively. These were very challenging projects but Helen made great strides in elucidating the structures of these components and working out how they are regulated and function. For example, in a landmark publication in 2011 Helen reported that a key regulatory role for the N-terminal ubiquitin-like domain of Parkin operated by binding to the catalytic domain as an auto-inhibitory domain. This discovery has provided great insights into how Parkin is regulated and functions. In another beautiful Nature Structural Molecular Biology paper in 2010, Helen was able to devise a strategy to express, crystallise and solve the structure or the Drosophila FANCL E3 ligase which reveals that the architecture of the domains turned out to be fundamentally different from previous sequence-based predictions. In 2013 Helen moved her laboratory to the MRC-PPU where she is continuing her work to better understand Parkin and FANCL and how these enzymes are linked to disease.

Commenting on the award Helen said “I am absolutely thrilled to be awarded the Colworth Medal. It is a wonderful endorsement of the efforts in my lab to understand the molecular processes underlying protein regulation.” MRC-PPU Director Dario Alessi stated “This is fantastic recognition for the ambitious and important research that Helen has undertaken to date. Her work has provided fabulous insights into key biochemical processes that are of great relevance to better understanding and treating diseases such as cancer and Parkinson’s disease. I am delighted that we have been able to recruit Helen to our Unit. Helen’s talent and ambitious future research plans particularly excite me. These show great promise and are likely to provide critical knowledge that could lead to improved strategies to better treat disease in the future.

Helen is the tenth principal investigator working within the College of Life Sciences at the University of Dundee to be awarded the Colworth medal. The previous recipients are Philip Cohen (1977), David M.J. Lilley (1982), Pete Downes (1987), Michael Ferguson (1991), Angus Lamond (1992), Dario Alessi (2000), Tom Owen-Hughes (2002), Frank Sargent (2007) and John Rouse (2008). In addition two other researchers who trained within the MRC-PPU, namely Nicholas C. Tonks (1993) and David Barford (1998), have also been awarded the Colworth medal.

The Colworth Medal is awarded annually since 1963, and Helen will be the 52nd recipient. Helen is only the third female researcher to receive this accolade.




 

MRC-PPU Clinical PhD Student awarded prestigious Clinical Lectureship
4 March, 2014
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Esther Sammler (and her daughter, Maya) discussing her FBX07 poster with Sir John Savill, CEO of the Medical Research Council

Esther Sammler, a Clinical PhD student supervised by Dario Alessi, has been appointed to a sought-after SCREDS Clinical Lectureship in Neurology at the University of Dundee. SCREDS (Scottish Clinical Research Excellence Development Scheme) lectureships enable talented young clinicians to combine research with clinical training.

Esther, who will defend her PhD in April, was previously awarded a highly competitive Wellcome Trust Clinical PhD Fellowship to undertake her PhD in Dario’s lab. During her PhD Esther has been investigating the function of the F-box protein, FBX07, in which mutations lead to Parkinson’s disease. Esther has made a number of exciting advances in her project including generating a novel transgenic mouse model containing a human disease-associated point mutation. Esther will take up her lectureship after she defends her PhD and will continue to investigate FBX07 in Dario’s lab as well as complete her clinical training towards becoming a Consultant Neurologist.

Commenting on the award, Dario said: “I am delighted for Esther in securing this prestigious clinical position that will enable her to continue her important studies on understanding FBX07. Over the last few years the MRC-PPU has placed a huge emphasis on training clinicians at both PhD and postdoctoral level. A common theme of PhD projects offered in the Unit is an emphasis on undertaking basic research to uncover molecular mechanisms underpinning human diseases including cancer, immunological and neurodegenerative diseases and our clinicians have made major contributions in these areas. Its very important for the future of UK medical research that our Unit does all it can to provide promising young clinicians with the opportunity to undertake cutting-edge fundamental research into understanding human disease.“

Esther is the fourth clinician to train for a PhD in the MRC-PPU and the second to be awarded a clinical lectureship upon completion. Kashyap Patel (supervised by Kei Sakamoto) was recently awarded a clinical lectureship at the University of Exeter Peninsula School of Medicine to undertake research in diabetes under the mentorship of Prof Andrew Hattersley FRS.




 

Janis Vogt, Ph.D. student in Gopal’s lab, publishes a paper on the discovery and functional characterisation of FAM83G/PAWS1
21 February, 2014
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Janis Vogt

Bone morphogenetic proteins (BMPs) control multiple cellular processes in embryos and adult tissues. BMPs signal through the activation of type I BMP receptor kinases, which then phosphorylate SMADs 1/5/8. In the canonical pathway, this triggers the association of these SMADs with SMAD4 and their translocation to the nucleus, where they regulate gene expression. BMPs can also signal independently of SMAD4, but this pathway is poorly understood.

Research undertaken primarily by Janis in Gopal Sapkota’s laboratory over the last three years has uncovered unique roles of FAM83G/PAWS1 (Protein Associated With SMAD1) in the BMP signalling pathway and beyond.

The key novel findings that his research has made are highlighted below:
• PAWS1 selectively interacts with SMAD1
• PAWS1 forms a complex with SMAD1 in a SMAD4-independent manner
• PAWS1 is phosphorylated by BMPR1A in response to BMP, making it the first non-SMAD substrate to be reported.
• The phosphorylation of PAWS1 in response to BMP is essential for activation of the SMAD4-independent BMP target genes NEDD9 and ASNS.
• Additionally, PAWS1 regulates the expression of several non-BMP target genes, suggesting roles for PAWS1 beyond the BMP pathway.

Lina Herhaus, Robert Gourlay, Thomas Macartney, David Campbell as well as collaborators Kevin Dingwell and Jim Smith (NIMR, Mill Hill, London) also contributed to this research.

The paper entitled “Protein associated with SMAD1 (PAWS1/FAM83G) is a substrate for type I bone morphogenetic protein receptors and modulates bone morphogenetic protein
signalling” can be accessed through Open Biology.
http://rsob.royalsocietypublishing.org/content/4/2/130210.short?rss=1

Janis successfully defended his Ph.D. thesis on 8th October 2013.

He is currently a postdoctoral research fellow in Prof. Thomas Jentsch’s laboratory at the Max-Delbrueck-Center for Molecular Medicine/Leibniz-Institute for Molecular Pharmacology in Berlin, Germany. He is investigating the mechanisms of ion homeostasis of different anion and cations in cellular organelles in order to understand the underlying molecular mechanisms of ion channel associated diseases.

Reference:

Vogt J, Dingwell KS, Herhaus L, Gourlay R, Macartney T, Campbell D, Smith JC, Sapkota GP (2014) Protein associated with SMAD1 (PAWS1/FAM83G) is a substrate for type I bone morphogenetic protein receptors and modulates bone morphogenetic protein signalling. Open Biol. 4:130210. http://dx.doi.org/10.1098/rsob.130210




 

Alastair Aitken – In Memoriam
13 February, 2014
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Alastair Aitken (L) and Philip Cohen (R) at Niagara Falls during the free afternoon of the 11th World Congress of Biochemistry, Toronto, Canada - 1979

The Unit has received the very sad news that Alastair Aitken, a former postdoc in the MRC Protein Phosphorylation Unit has died from pancreatic cancer. Alastair was born in Dundee and left High School at the age of 16 to work in an oil company in the Dundee shipyards. Several years later, he decided to go to University receiving a B.Sc in Chemistry with First Class Honours from Heriot-Watt University, Edinburgh, and an M.Sc in Microbiological Chemistry at the University of Newcastle. He obtained a Ph.D. in the Department of Molecular Biology at the University of Edinburgh under the supervision of Richard Ambler, where he learned how to sequence proteins, and then spent four years at the Institut Pasteur, Paris, initially as a postdoctoral fellow and then as “Charge de Recherche” in the Division of Virology. He seemed destined to spend the rest of his career at the Institut Pasteur as head of Protein Chemistry. However, a new Director was appointed at Pasteur, who decided that setting up a new protein sequencing facility was not his highest priority and so, much to his surprise and amusement, Alastair found himself back in the town of his birth in late 1978, where Philip Cohen had just obtained the funding to purchase a Beckman Liquid Phase Protein Sequencer, one of a handful of automated protein sequencers in the UK.

The five years that Alastair spent in Philip’s lab were highly productive and the 16 papers that Alastair published over this period led to Dundee becoming recognized as Europe’s premier location for the identification of phosphorylation sites in proteins. Identifying phosphorylation sites in those days was challenging but, over the period 1980-1982, Alastair managed to identify all the phosphorylation sites on glycogen synthase that were phosphorylated by the protein kinases glycogen synthase kinase 3 (GSK3), cyclic AMP-dependent protein kinase (PKA) and casein kinase 2. This led to glycogen synthase becoming the paradigm for “multisite phosphorylation”. It also paved the way for the discovery that insulin activates glycogen synthase by inducing dephosphorylation of the sites targeted by GSK3; this in turn led to elucidation of the mechanism by which insulin inhibits GSK3 in the 1990s. Alastair went on identify many serine and threonine residues in proteins that are phosphorylated specifically by PKA or by cyclic GMP-dependent protein kinase (PKG) enhancing our understanding of the similarities and differences in the ways that these protein kinases recognize their substrates. In two further major pieces of work, Alastair determined the entire amino acid sequences of Inhibitor-1 and contributed to the determination of the sequence of inhibitor-2, two specific protein inhibitors of protein phosphatase 1. He also determined the entire amino acid sequence of the B-subunit of calcineurin, a calcium/calmodulin-dependent protein phosphatase. In 1982, Alastair discovered that the N-terminal glycine residue of calcineurin B was blocked with a myristyl group, the same year that Koiti Titani’s lab found that the N-terminal glycine residue of PKA was myristylated: these were the first two examples of N-myristoylated proteins.

The outstanding work that Alastair carried out in what was then called the MRC Protein Phosphorylation Group at Dundee, led to his appointment as a Lecturer in the School of Pharmacy at the University of London, and later as a Principal Investigator at the National Institute for Medical Research, London. David Campbell, Alastair’s successor in the MRC-PPU said today that he greatly appreciated all the work that Alastair had put into building up an excellent protein chemistry laboratory, something that had made David’s job so much easier after he joined us. He also commented that, even after Alastair left Dundee, he was always willing to spend time sharing his experiences and discussing various research problems relating to his time in Dundee.

Alastair returned to Scotland in 1999 as the Professor of Protein Biochemistry at the University of Edinburgh. In his own laboratory, Alastair gained a major international reputation for his pioneering work on the 14-3-3 proteins that interact specifically with phosphorylated motifs in hundreds of proteins. He discovered that the ability of 14-3-3 isoforms to form stable dimers is critical for their regulatory actions, and that the dysregulation of 14-3-3 proteins contributes to CJD, Spinacerebellar ataxia and other neurodegenerative diseases. By generously sharing his reagents with other investigators, and by hosting several extremely successful conferences, Alastair was instrumental in building up a strong community of scientists who are now uncovering an impressive diversity of roles for 14-3-3 proteins in plants and yeast, as well as mammals. His first Ph.D. student was Nick Morrice, who later became the Head of Protein Chemistry in the MRC Protein Phosphorylation Unit setting up and running the Unit’s mass spectrometry facility for many years.

Alastair had a passion for science and a real feel for proteins and how they work. He was warm and friendly and made lasting friendships with many other members of the laboratory. He also had a unique and wry sense of humour. With his quiet voice and broad Dundonian accent he could sometimes be difficult to understand and, in reference to the years he had spent in Paris, it was a standing joke in the Unit that Alastair spoke much better French than English, a remark that never failed to bring a smile to his face! Alastair will be sadly missed and we send our condolences to his wife Michele and four children.




 

Dario Alessi to deliver 2014 Sackler Lecture
4 February, 2014

The Academy of Medical Sciences announced this week that MRC-PPU Director Dario Alessi will deliver the Raymond and Beverly Sackler Distinguished Lecture in the Medical Sciences on 2 July 2014, as part of the annual Fellows Admission Day. Dario was elected as a Fellow of the Academy in 2012.

Dario's lecture, entitled 'Disruptions on the Highways of Cell Communications', is open to all. He will then deliver the Sackler Lecture at the Cambridge Clinical School on 3 July 2014.

The Sackler Distinguished Lecture series was established through a generous endowment given by Raymond and Beverly Sackler to the Academy of Medical Sciences in 2003. Raymond and Beverly Sackler are international philanthropists with a deep longstanding commitment to supporting scientific research. The Sacklers have been dedicated sponsors of basic biomedical research as well as many other areas of intellectual pursuit.

The lecture provides a platform for internationally renowned speakers from the medical sciences and promotes debate, discussion and the exchange of ideas on current research.

Previous speakers who have also delivered the CLS named lectures include, Dr Venki Ramakrishnan FRS FMedSci, MRC Laboratory of Molecular Biology
 (2011), Professor Sir David Baulcombe FRS FMedSci, University of Cambridge
 (2010) and Professor Elizabeth Blackburn FRS University of California San Francisco
 (2009).

Tickets must be booked in advance. For more information, including how to book, visit the Society’s event page or contact info@acmedsci.ac.uk.




 

2013 Tim Hunt prize for Cell Biology awarded to Lina Herhaus
30 January, 2014
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Lina being awarded her prize by Dean of Research, Mike Ferguson, at the CLS Review of the Year

Congratulations to Lina Herhaus, PhD student in Gopal Sapkota's lab, on being a recipient of the 2013 Tim Hunt Prize for Cell Biology for her work on elucidating the role of OTUB1 in the TGF-beta pathway.

The Tim Hunt prize for Cell Biology is awarded for a significant advance in basic research in any area of cell biology carried out in the College of Life Sciences at the University of Dundee. The award committee awarded the prize to Lina “for a tour de force performance in the first two years of her PhD research to improve our general understanding of TGF-beta signalling”. Lina’s research was published in Nature Communications.

Upon receiving the award, Lina said, “I am so happy to have been a winner of the Tim Hunt prize this year, as it gives me even more confidence in my research. It is brilliant to see that my findings have been recognised as important contributions to the field of cell biology. It really is a great honour for me and I am very thankful to my supervisor Gopal Sapkota for his guidance and to all members of the MRC PPU for their support.”

MRC-PPU Director Dario Alessi commented, “I am delighted that Lina has received this extremely prestigious accolade. Lina is a remarkably talented and creative young researcher who is undertaking important fundamental research in Gopal Sapkota’s lab on how the TGFbeta signalling pathway is regulated and functions. Lina’s work provides intriguing new insights into how this pathway impacts on cancer. I am confident that Lina’s research will make a major mark in this vital field of research”.

Lina is the third MRC-PPU researcher to receive the Tim Hunt prize in the last four years. Other winners were Shuai Chen (2011, supervised by Carol MacKintosh) and Anna Zagorska (2010, supervised by Dario Alessi).




 

Karim Labib receives prestigious award from the Wellcome Trust
16 January, 2014

Congratulations to Karim Labib, who has just been awarded a Senior Investigator Award by the Wellcome Trust, which will amount to £1.8 million of funding over the next five years. These awards are intended to provide flexible support to the best researchers, in order to address some of the most important questions about health and disease.

Karim joined the MRC-PPU in October and his research group studies how the eukaryotic replisome allows cells to preserve their genome integrity and epigenetic information. This award from the Wellcome Trust will allow Karim's group to study the mechanisms of the eukaryotic replisome, complementing their MRC-funded work regarding the regulation of the replisome by ubiquitylation and phosphorylation.

Commenting on the award Karim said, "I am very grateful to the Wellcome Trust for their support, and this award will be extremely important for my lab. It makes perfect sense for us to study the mechanisms of the eukaryotic replisome in parallel with studying its regulation by post-translational modifications, and we now have the funding in place to do both. I am sure that the MRC-PPU and the College of Life Sciences will provide an ideal environment for our work."

Dario Alessi, Director of the MRC Unit added "I am thrilled that Karim has been able to secure prestigious Wellcome Trust funding to support his elegant research on understanding the molecular mechanism that controls the replication of DNA in Eukaryotes. This is an amazingly intricate and fundamental process. Karim's work has great potential to reveal innovative findings that that lead to critical insights into diseases such as cancer".




 

New role for the hypertension WNK-regulated SPAK/OSR1 kinases in controlling chloride influx
10 January, 2014

Much work in Dario Alessi’s lab over the last 10 years has focused on understanding the function and regulation of the WNK1 and WNK4 family of protein kinases whose overexpression in humans causes Gordon’s hypertension syndrome. Patients with this condition suffer from high blood pressure and hyperkalemia (high serum potassium), and can be treated using thiazide diuretic hypertension drugs that inhibit the NCC ion co-transporter in the kidney.

Work from the Alessi lab, as well as other labs, has revealed that the WNK enzymes are activated in response to hyperosmotic stress such as hypotonic low chloride conditions and phosphorylate and activate two other closely related protein kinases termed SPAK and OSR1. Once activated SPAK and OSR1 promote chloride influx into cells by phosphorylating and stimulate the activity of 3 cation-Cl- co-transporters collectively termed N[K]CCs which comprise NKCC1 (expressed in all cells), NCC or NKCC2 (expressed in the kidney).

Mutations that increase expression of WNK1 and WNK4 therefore cause hypertension by inducing too much activation of the SPAK/OSR1 kinases, which in turn result in over-stimulation of NCC and NKCC2 leading to inappropriately high salt retention in the kidnet. This also explains why thiazide diuretics that inhibit NCC are so effective at lowering blood pressure in Gordon syndrome patients.

It turns out that although N[K]CCs play a critical role in regulating intracellular chloride concentration –enzymes that catalyse the opposite reaction namely those controlling chloride efflux also play an important role. The enzymes that control chloride efflux are called KCCs and are also cation-Cl- co-transporters.

Much previous work has suggested that the activity of N[K]CCs and KCCs are coordinately regulated. ie conditions that stimulate net chloride influx (e.g. hypotonic low chloride) activate N[K]CCs and inhibit KCCs. Vice versa conditions that stimulate net chloride eflux (e.g. hypotonic high potassium) inhibit N[K]CCs and activate KCCs. Moreover, as discussed above phosphorylation activates N[K]CCs, but in contrast, phosphorylation by unknown kinases inhibits KCCs. Conversely, dephosphorylation inhibits N[K]CCs but activates KCCs. This reciprocal and opposite regulation of Na+- and K+-driven CCCs - ensures that cellular Cl- influx and efflux is tightly coordinated and this mechanism is conserved from worms to man.

Previous seminal work by Jesse Rinehart and Richard Lifton at Yale revealed that activity of KCCs is critically controlled by phosphorylation of two highly conserved residues (termed Site-1 and Site-2) located within the intracellular C-terminal domain of these enzymes.

The identify of the kinases phosphorylating these vital sites on KCC isoforms were not known. Paola de los Heros and Jinwei Zhang, postdocs in the Alessi lab, in collaboration with Kris Kahle at Harvard University therefore set out to search for kinases that regulate KCCs. In the first part of this work they have now excitingly discovered that it is the WNK-regulated SPAK/OSR1 kinases that directly phosphorylate Site-2 on all KCC isoforms, thereby leading to the inhibition of the K+-Cl- co-transporters. Firstly, Paola discovered that SPAK and OSR1, in the presence of the MO25 regulatory subunit, robustly phosphorylated all KCC isoforms at Site-2 in vitro. Secondly, Jinwei found that STOCK1S-50699, a WNK pathway inhibitor, suppressed SPAK/OSR1 activation and both overexpressed and endogenous KCC3A Site-2 phosphorylation with similar efficiency. Thirdly, in embryonic stem cells lacking SPAK/OSR1 activity Paola and Jinwei discovered that endogenous phosphorylation of KCC isoforms at Site-2 is abolished and these cells display elevated basal activity of 86Rb+. Finally Jinwei established that there was a tight correlation between SPAK/OSR1 activity and the magnitude of KCC3A Site-2 phosphorylation. Paola also observed that KCCs are directly phosphorylated by SPAK/OSR1, at a novel Site-3 (Thr5 KCC1/KCC3 and Thr6 KCC2/KCC4), and a previously recognised KCC3-specific residue, Site-4 (Ser96).

These data demonstrate the WNK-regulated SPAK/OSR1 kinases directly phosphorylate the N[K]CCs and KCCs, promoting their stimulation and inhibition, respectively.

Given these reciprocal actions with anticipated net effects of increasing chloride influx, the new data suggests that targeting of WNK-SPAK/OSR1 with kinase inhibitors might comprise a new strategy to enhance cellular chloride extrusion. This has potential implications for the therapeutic modulation of epithelial and neuronal ion transport in human disease states.

In future work it will be exciting to identify the kinase that regulates KCCs at Site-1 and work out whether this is regulated by WNK isoforms.

To read a copy of Paola and Jinwei’s paper click here




 

Helen Walden published first paper since joining MRC-PPU
9 January, 2014
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Charlotte Hodson

Helen Walden's lab studies the molecular mechanisms that control attachment of ubiquitin (a protein tag or signal) to its targets. Attachment requires the sequential action of 3 enzymes, E1, E2 and E3. E2s and E3s interact with each other to allow the final step of transfer to target. The problem is that there are ~40 E2s and ~600 RING-type E3s in the human genome, which gives rise to thousands of possible E2-E3 pairs. Yet there are pathways in which the E2-E3 pair is exclusive and the basis of this exclusivity/specificity is poorly understood on a molecular level.

The Walden lab uses the Fanconi Anemia (FA) DNA repair pathway as a model for understanding specific ubiquitination events. FANCL (an E3) and Ube2T (an E2) team up to stick one molecule of ubiquitin onto the target FANCD2. If this attachment does not occur, Fanconi Anemia develops. FA is a rare but deadly childhood disorder that results in genomic instability, bone marrow failure, and a high predisposition to cancer. FANCL is not known to function with E2s other than Ube2T, and Ube2T has not yet been found to function physiologically with other E3s. Therefore Charlotte Hodson, a recent PhD student in the Walden lab, determined the high-resolution crystal structure of FANCL in complex with Ube2T, and discovered that in addition to the interface commonly seen between E2s and E3s, there are a number of extra interactions that make this pairing specific, in particular a key charge-charge interaction that we find is required for FANCL/Ube2T function.

The resulting paper contains data generated at the London Research Institute of Cancer Research UK and at the MRC Protein Phosphorylation and Ubiquitylation Unit, and has just been published in Structure - click here to view.




 

Sonal Das Joins the MRC-PPU
7 January, 2014

We warmly welcome Sonal Das, who joined the MRC-PPU on Monday 6th January.

Sonal will play a major role in helping to further develop the MRC-PPU. This will include organising our public engagement in science activities, taking charge of the MRC-PPU Reagents website, coordinating major MRC-PPU projects/collaborations, helping to develop and improve MRC-PPU scientific services, and aiding our unit's PIs with grant funding applications.

Sonal was previously a Senior Associate Director of the Michael J Fox Foundation for Parkinson's Research (MJFF) in New York City (2009-2013), which is the world's largest foundation supporting Parkinson's disease research. Here she oversaw and coordinated many of the MJFF grant funding programmes. A major part of Sonal's work at the MJFF also involved interacting with Parkinson’s researchers from many different institutions, organising research review meetings to evaluate progress and identify new areas for research. She led initiatives to develop novel tools and reagents for PD research (including antibodies and viral vectors) and facilitated collaborations between researchers in industry and academia. Finally, Sonal was also involved in presenting information about Parkinson’s research to the general public and to potential donors.

Prior to working in the MJFF Sonal did her PhD project in the laboratory of Gary Banker at Oregon Health and Science University (2000-2005) where she worked on understanding trafficking motifs regulating dendritic receptor localisation in primary hippocampal neurons. Sonal subsequently did a postdoc with Stan Froehner at the University of Washington (2006-2009), where she studied the trafficking of aquaporin-4, a water channel expressed by astrocytes that selectively localizes to the blood brain barrier and regulates water homeostasis between the vasculature and cellular components of the brain and is thought to play a key role in the brain edema that occurs after trauma or stroke. Sonal established a cell culture system to evaluate the localization and trafficking of aquaporin-4, developed reagents for live cell imaging of this protein, and examined the trafficking of aquaporin 4 was altered by oxygen/glucose deprivation.