About BEB
CNC Research
BEB in the Media
Biology of Proteolysis
November 24 - 28
Sandra M. Cardoso, Cláudia Pereira, Paulo Pereira
Organizers:Sandra Morais Cardoso (smacardoso@yahoo.com); Cláudia Pereira (claudia.mf.pereira@gmail.com); Paulo Pereira (ppereira@ibili.uc.pt)

Ana Maria Cuervo (Albert Einstein College of Medicine, New York, USA)
Cláudia Pereira (Universidade de Coimbra, Coimbra, Portugal)
Michael Clague (University of Liverpool, Liverpool, UK)
Paulo Pereira (Universidade de Coimbra, Coimbra, Portugal)
Sandra Morais Cardoso (Universidade de Coimbra, Coimbra, Portugal)
Sylvie Urbe (University of Liverpool, Liverpool, UK)

Organization and Goals
The Course lectures will be open to the general public and Journal Club/Grant Proposal discussions will be made by student with pre-assigned papers/themes. Those are open to all CNC-PhD students, not only BEB students. Who wish to attend/be evaluated (please contact the course coordinator).
Students will have access to papers that will be made available (in BEB’s page) previous to the course.
Presentations should be prepared and given together. Prepare a PowerPoint file that should contain copies of most or all figures in the paper.

Monday, November 24
9h30: Introduction to the course, summary of course goals and student goals.
10h00-11h00: Introduction to the Ubiquitin-Proteasome System
Paulo Pereira
11h00-11h15: Break
11h15-12h15: Ubiquitin-Proteasome System: Applications to Biomedicine
Paulo Pereira

15h00-17h00: Tutorial distribution of papers relevant to the course.

Tuesday, November 25
9h30-10h30: Deubiquitinating Enzymes I
Sylvie Urbe or Michael Clague
10h30-10h45: Break
10h45-11h45: Endoplasmic Reticulum Associated Protein Degradation
Sylvie Urbe or Michael Clague
11h45-12h00: Break
12h00-13h00: Deubiquitinating Enzymes II
Sylvie Urbe or Michael Clague
15h00-17h30: Journal Club/Grant Proposal
Wednesday, November 26
9h30-10h30: Nuclear Function of Ubiquitin I
Sylvie Urbe or Michael Clague
10h30-10h45: Break
11h00-12h00: Nuclear Function of Ubiquitin II
Sylvie Urbe or Michael Clague
14h00-15h00: Introduction to autophgy and main autophagic pathways
Ana Maria Cuervo
15h00-15h45: Break
15h45-17h45: Journal Club/Grant Proposal

Thursday, November 27
9h30-10h30: Autophagy in disease and aging
Ana Maria Cuervo
10h30-10h45: Break
10h45-11h45: Endocytosis I
Sylvie Urbe or Michael Clague
11h45-12h00: Break
12h00-13h00: Endocytosis II
Sylvie Urbe or Michael Clague
15h00-17h30: Journal Club/Grant Proposal
18h00: Social Event
Friday, November 28
10h00-11h00: ER involvement in autophagy
Cláudia Pereira
11h00-11h15: Break
11h15-12h15: Mitochondrial role in the autophagic process
Sandra Morais Cardoso
16h00:CNC Seminar Pathophysiology of chaperone-mediated autophagy
Ana Maria Cuervo
Confirmed Invited Speakers
Ana Maria Cuervo (Associate Professor, Department of Developmental and Molecular Biology, Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA)
Mizushima N, Levine B, Cuervo AM, Klionsky DJ. Autophagy fights disease through cellular self-digestion. Nature. 2008 Feb 28;451(7182):1069-75. Review.
Bandyopadhyay U, Kaushik S, Varticovski L, Cuervo AM. The Chaperone-Mediated Autophagy Receptor Organizes in Dynamic Protein Complexes at the Lysosomal Membrane. Mol Cell Biol. 2008 Jul 21
Massey AC, Kaushik,S., Sovak, G., Kiffin, R.& Cuervo, AM. Consequences of the selective blockage of chaperone-mediated autophagy. Proc Nat Acad Sci USA 103, 5905-5910 (2006)

Michael Clague (Professor, University of Liverpool, Liverpool, UK)
Lorenzo O, Urbé S, Clague MJ.Systematic analysis of myotubularins: heteromeric interactions, subcellular localisation and endosome related functions.J Cell Sci. 2006 Jul 15;119(Pt 14):2953-9. Epub 2006 Jun 20.
Lorenzo O, Urbe S and Clague M J (2005) Analysis of phosphoinositide binding domain properties within the myotubularin-related protein MTMR3. J Cell Sci,118(Pt 9),pp.2005-12
Carter S, Urbe S and Clague M J (2004) The met receptor degradation pathway: requirement for Lys48-linked polyubiquitin independent of proteasome activity. J Biol Chem,279(51),pp.52835-9
Sylvie Urbe (Cancer Research UK Senior Research Fellow, University of Liverpool, Liverpool, UK)
McCullough J, Row P E, Lorenzo O, Doherty M, Beynon R, Clague M J and Urbe S (2006) Activation of the endosome-associated ubiquitin isopeptidase AMSH by STAM, a component of the multivesicular body-sorting machinery. Curr Biol,16(2),pp.160-5
Row P E, Prior I A, McCullough J, Clague M J and Urbe S (2006) The Ubiquitin Isopeptidase UBPY Regulates Endosomal Ubiquitin Dynamics and Is Essential for Receptor Down-regulation. J Biol Chem,281(18),pp.12618-24
Row PE, Liu H, Hayes S, Welchman R, Charalabous P, Hofmann K, Clague MJ, Sanderson CM, Urbé S.The MIT domain of UBPY constitutes a CHMP binding and endosomal localization signal required for efficient epidermal growth factor receptor degradation. J Biol Chem. 2007 Oct 19;282(42):30929-37. Epub 2007 Aug 21.
To present and/or criticize a paper you should take in consideration these aspects:
- Read the paper ahead of time, and decide what you think of the ideas presented in the paper. In particular, decide whether you think the paper has some good ideas or whether determine what you think is the central fallacy or bad idea.
- Next, decide which idea(s) is(are) the best idea(s) (most novel, most central, most relevant, most clever, most important…) in the paper. Write down this(these) idea(s), preferably in your own words, and a one-line justification for why this idea is the best one.
- The crucial step is to figure out how to get your audience as quickly as possible to the point where they can understand this idea.
Next, think why the project was done at all, what it added to the literature, what controls were done or neglected, whether the claims of the paper were justified and sustained by later work, whether the experiments were technically sound and convincing, and what alternative ideas might have been pursued instead.
Grant Proposals
Presentation should be prepared together and given together—one presentation, essentially. Presenters should compose a brief draft of a mock grant or fellowship proposal. Three specific Aims is often a good number though anywhere from 2-5 can be quite reasonable. These aims should be listed in bullet point form underneath the title of the proposal. You may also employ sub-aims if you prefer (Aim 1A, Aim 1B, etc). Take care that the proposal has a sensible structure: the title should outline the major and general aim, which should be accomplished via several more specific aims, which themselves will be achieved by means of specific experiments.
The proposal should not entirely hinge on one experiment that may or may not work. The proposal should not be narrow but should address a significant issue in a deep manner, leading to a new level of understanding of that problem. A clearly defined hypothesis will help in developing your proposal. The text version of the proposal should be one page maximum, essentially an abstract of the proposal. Normally grants work within the framework of a specific number of man-years to perform, anything from 3-6 man-years is most reasonable, but it is really up to you. Shorter is better, all things being equal, so that you can do justice to individual experiments. Estimate the number of man-years but it is not a big deal.
The subject matter should be related in some way to the paper presented on that day, but does not have to be direct follow up work. Direct follow-up is OK too but make sure there are new ideas there. Do not hesitate to discuss whether a general proposal idea is appropriate with course faculty, but faculty input should be only general, they should not “fashion” the proposal actively in advance. If you wish to work on this in advance of the course meeting, you can contact them by email. Feasibility and creativity are both important in evaluating the proposal, but creativity more so. Try not to only propose familiar experiments. Consider multiple approaches for testing your hypothesis (for example, combining genetic and biochemical approaches). Prepare a powerpoint presentation outlining the proposal and diagramming some of the central experiments you propose. Consider in this powerpoint version necessary controls and pitfalls, and the significance of the project you propose. Non-presenters should discuss the merits of the proposed experiments—whether the problem is a good one, whether the experiments effectively address the problem and will give interpretable results, whether they could actually be done in practice, whether necessary controls have been provided, whether still other experiments should be considered, and, assuming that everything goes to plan, whether the information gained would deliver a significant advance in our understanding of the subject matter.
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