Biochemistry III Proposal seminar

Transcription

1 Biochemistry III Proposal seminar

2 BCIII Seminar Research Proposals What is a Research Proposal? What is the purpose of this Seminar? How is this Seminar organized / conducted? How do I define a proposal topic? How do I arrange and prepare my proposal?

3 What is a Research-Proposal? Written form of a future research project: - for a Diploma- or PhD thesis (e.g. to prepare yourself for a research project, or to apply for a stipend) - application for research funds Drittmittel As a quality control: Usefulness and Feasibility of the planned research - allocation of research funds (DFG, BMBF, EU, Foundations for Stipends) - Internal control (e.g. for prospective PhD students) Is presented / proposed to a group of reviewers Begutachtung - Internal assessment (colleagues, co-workers, supervisors) - External (anonymous) reviewers It is important that reviewers critically look into the proposal, to uncover weaknesses, such that better (revised) proposal can be prepared

4 Important question for a Research Proposal What have we learned after successfuly finishing of the project (or which page in the text book has to be added or corrected?) Why is this work important for my research area? Are the applied strategies the best one?

5 What is important for a Research Proposal? Important: The reviewers are most often no experts in exactly the same research field - thus, a focussed introduction into the topic should be given The reviewer needs to be convinced that the research topic is relevant, and that it is important to study the given problem! - thus the objectives need to be clearly worked out The reviewer needs to be convinced that the research plan can be conducted the way it is proposed, and in the time frame that is proposed! - methodological approaches need to be carefully and critically worked out / elaborated on

6 Goals of this Seminar Work out and present a current topic in biochemical research Utilize various modern methods on a current scientific question Critical discussion of a research project Estimate a realistic time frame for the proposed project Work out a written description of a research proposal

7 Preparation Each week, a group of 2-3 students will prepare for one of the given topics Based on the current state of the art, they will define and formulate an important, novel question in this research field Based on available literature, the group will get familiar with special methods that are of central importance for the respective research topic The students will work out a presentation that describes the background, scientific problem and the way they want to tackle this problem A second group of students will act as the Reviewers, and will prepare themselves for the topic and methods, based on the presentation of the first group They try to identify weak points in the work program, and plan for a structured discussion

8 Sequence of events Structure of the Presentations (in English) Introduction into the topic (ca. 15 min) Introduction of relevant methods (ca. 15 min) Presentation of the proposal and work program (ca. 15 min) 5 min. break, such that ALL participants may reflect on the proposal Discussion of the proposal (may be done in German or English) critical evaluation of the proposal ( Review ) moderated and structured by the Reviewer-Group constructive suggestions for improvements

9 The question: How do I get to my proposal? - points that are not yet well understood in a particular research field are often explicitely pointed out in review articles - Try formulating a very specific question, rather than wishing to understand everything, somehow - thus, projects aiming at proteomics, structure determination, genetic or RNAi screens, screens for new drugs, micro-array profiling, etc. are not very useful as a central question. Rather, formulate a hypothesis-driven question.

10 How do I get to my proposal? The methods: - how do I get as many insights as possible with as little effort as possible in a short time? - again, work out very specifically how a particular problem can be tackled - can I use DNA-constructs, cell-lines, organisms or techniques for more than just one experiment of interest? Can I get such starting material from others? - How do I continue after a particular experiment ( if, then )? - How can I use complementary approaches to verify a result?

11 Written Elaboration Getretener Quark wird breit, nicht stark don t know how to translate this 1. Summary / Abstract (max. ½ page) 2. Background / State of the art (1-2 pages) 3. Objectives (ca. ½ page) 4. Workplan (ca. 3 pages) 5. Literature / References

12 Summary Is written as the very last part of the proposal (i.e. when you know exactly what you need to summarize) Summarizes the proposal as a whole, just like the abstract of a scientific paper 1-2 sentences for background and motivation 1-2 sentences for objectives Ca. 5 sentences about experimental approaches that you would like to follow

13 Background / State of the art Contains important background knowledge, as already described in the presentation Important: lead the reader from a brief description of the general background to the specific question do not dump facts over facts that are not directly relevant! Goal: the question worked out should be highly relevant in the particular field Presented facts and hypotheses must be supported by referenced literature A good schematic from a review article can deliver a lot more knowledge and understanding than a 1000 words can nevertheless, they need to be described with a few words, either in the text (reference the figure!) and/or in the figure legend If you use figures from a publication, you need to reference the source of this figure

14 Objectives This part of the proposal is most likely the one that is read first by the reviewer absolutely central! 1-2 sentences: which scientific questions shall be answered by the results of this research project? 2-4 sentences: briefly describe, which methodological approaches are chosen, and how they will answer the particular question

15 Work Program Main part of the proposal, give a relatively detailed description of your approach Step by step explain the methodological approach, discuss possible results, and limitations, alternatives Do not give exact protocols of the methods, but say e.g.: - which vector you will use, which cell line you chose, and why? - which measuring technique, which measured variable do you chose, and which conclusions follow from this? - Which controls do you perform, to verify and support your results? - Which alternatives are available?

16 Formalities Title page (clear and short title, address, picture) Figures need to be numbered and have a legend, and they have to be carefully referenced in the text (use Word Tools!) Use consistent fonts and text sizes for: - headings - main text - Legends - cited literature Reference literature in the text and in the reference list has to be consistent! (use citavi) Further tips on how to write a proposal: Leitfaden from R. Jahn (MPI Göttingen), will be distributed by

17 Structure / schedule of the seminar Start of the seminar: 8:15 h am At least 2 weeks before your proposal date: meet with supervisor for a preparatory meeting Vorbesprechung Meet one or two more times to discuss the worked out proposal and presentation 1 week before your proposal date: Send around a review article about your research topic to the other students The day before your proposal presentation: prepare hand-outs for your presentation (4 slides per page) At the day of presentation: Set up Computer and Beamer (meet with supervisor at 8:00 h am Reviewer Group: ca. 1 week prior to the proposal date, meet with supervisor and presenting group for a brief presentation of the proposal

18 After the seminar Hand in the written proposal 2 weeks after the presenation (to supervisor & R. Abele) Final, corrected version one week after receiving feedback from the supervisor (again to supervisor & R. Abele)

19 Conclusion of the seminar / 6th semester: Individual research proposal To conclude the semester each student prepares an INDIVIDUAL PROPOSAL Topic can be freely chosen, should not be too close to the topics of the group proposals during the seminar (mainly biochemistry) Help / Tips can be requested from the Supervisors of this seminar; also Prof. Gottschalk, Prof. Ludwig, Prof. Pos, Prof. Tampé The proposal is worked out in writing (English) Hand it in by 18th Oktober 2010), electronically with Mrs. Le Gal (legal@em.uni-frankfurt.de) ca. 2 weeks later (exact dates will be fixed in time), the proposal will be orally defended, reviewers are one Professor of Biochemistry as well as a Beisitzer corrected version has to be submitted 2 weeks later, again to Mrs. Le Gal get your Schein

20 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

21 1. sirna Biology: from gene silencing to gene-specific therapeutics RNAi: intracellular mechanism triggered by different effector molecules Incorporation into the RNA-induced silencing complex (RISC) Target mrna cleavage and degradation Exploration of RNAi in vitro and in vivo?

22 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

23 2. Reversible switchable fluorescent proteins Recently, reversibly switchable fluorescent proteins (RSFPs) have attracted great attention. RSFPs can switch between a non fluorescent and a fluorescent state by lightirradiating. This characteristic makes them an ideal flourophor with unique properties for optical labelling in an spatio temporal manner.

24 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

25 3. AAA-ATPase in protein unfolding Enzyme consuming ATP, that unfolds proteins, e.g. in the proteasome

26 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

27 4. The Macromolecular Peptide Loading Complex

28 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

29 5. ABCE1 function in ribosome recycling essential protein involved in: translation initiation translation termination ribosome biogenesis ribosome recycling HIV capsid assembly.

30 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

31 6. Membrane insertion of tail anchored proteins posttranslational membrane insertion C-terminal transmembrane helix different pathways for insertion postulated

32 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

33 7. Intramembrane protein cleavage by the γ-secretase important event in the cleavage of APP to produce amyloid-β?

34 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

35 7. Membrane fusion viral factors & SNAREs How do enveloped viruses enter into host cells?

36 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

37 9. Transmembrane communication within bacterial two component systems Displacements of TMHs Rotation of TMHs

38 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

39 10. Viral immune escape strategies HIV glycoproteins & inhibition factors What is the funtion of......the glycan shield?...the hypervariability?...viral factors like Vpu?

40 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

41 11. Chaperone mediated autophagy lysosomal pathway to degrade long living cytosolic proteins strongly induced under stress conditions

42 Introduction --- sirna Biology: From gene silencing to gene specific therapeutics (Katharina Ceh) Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke) AAA-ATPase in protein unfolding The macromolecular peptide loading complex ABCE1 function in ribosome recycling Membrane insertion of tail anchored proteins Intramembrane protein cleavage by the γ-secretase complex How do enveloped viruses enter into host cells? Transmembrane communication within bacterial two-component systems (Roger Daheim) Viral immune escape strategies Chaperone-mediated autophagy: The way to survive starvation Protein translocation into peroxisomes (Peter Mayerhofer)

43 12. Protein Translocation Into Peroxisomes cytoplasmic polyribosomes Peroxisomal proteins are imported post-translationally membrane proteins matrix proteins The peroxisomal matrix protein import machinery accommodates fully folded / oligomeric proteins Peroxisomal proteins are recognized by receptors (e.g. PEX5) in the cytosol lipids peroxisome