Biochemistry III – Proposal seminar

Biochemistry III – Proposal seminar

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?

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 beprepared

• What have we learned after successfuly finishing of the project (orwhich 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?

Important question for a Research Proposal

What is important for a Research Proposal?

Important: The reviewers are most often no experts in exactly thesame research field- thus, a focussed introduction into the topic should be given

The reviewer needs to be convinced that the research topic isrelevant, 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 beconducted the way it is proposed, and in the time frame that isproposed !- methodological approaches need to be carefully and criticallyworked out / elaborated on

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

Preparation

Each week, a group of 2-3 students will prepare for oneof 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 withspecial methods that are of central importance for therespective research topic

The students will work out a presentation that describes thebackground, scientific problem and the way they want to tacklethis problem

A second group of students will act as the „Reviewers“, and will prepare themselves for the topic and methods, based on thepresentation of the first group

They try to identify weak points in the work program, and plan for a structured discussion

Sequence of events

Introduction into the topic (ca. 15 min)

Introduction of relevant methods (ca. 15 min)

Presentation of the proposal and work program (ca. 15 min)

critical evaluation of the proposal(„Review“) moderated and structured by the„Reviewer-Group“

constructive suggestions for improvements

Structure of the Presentations (in English)

Discussion of the proposal (may be done in German or English)

5 min. break, such that ALL participants may reflect on the proposal

How do I get to my proposal ?

The question:

- points that are not yet well understood in a particular research field are oftenexplicitely 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 orRNAi screens, screens for new drugs, micro-array profiling, etc. are not veryuseful as a central question. Rather, formulate a hypothesis-driven question.

How do I get to my proposal ?

The methods:

- how do I get as many insights as possible with as little effort as possiblein 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 thanjust 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?

Written Elaboration

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

„Getretener Quark wird breit, nicht stark“

don‘t know how to translate this…

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 abstractof a scientific paper

1-2 sentences for background and motivation

1-2 sentences for objectives

Ca. 5 sentences about experimental approaches that youwould like to follow

Background / State of the art

Contains important background knowledge, as alreadydescribed in the presentation

Important: lead the reader from a brief description of thegeneral 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 byreferenced literature

A good schematic from a review article can deliver a lot more knowledge and understanding than a 1000 wordscan – nevertheless, they need to be described with a fewwords, either in the text (reference the figure!) and/or in thefigure legend

If you use figures from a publication, you need to referencethe source of this figure

Objectives

This part of the proposal is most likely the one that is readfirst by the reviewer – absolutely central !

1-2 sentences: which scientific questions shall be answeredby the results of this research project ?

2-4 sentences: briefly describe, which methodologicalapproaches are chosen, and how they will answer theparticular question

Work Program

Main part of the proposal, give a relatively detailed descriptionof your approach

Step by step explain the methodological approach, discusspossible 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 andsupport your results ?

- Which alternatives are available ?

Formalities

Title page (clear and short title, address, picture)

Figures need to be numbered and have a legend, and they have to be carefullyreferenced 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 email

Structure / schedule of the seminarStart of the seminar: 8:15 h am

At least 2 weeks before your proposal date: meet with supervisor fora 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 articleabout your research topic to the other students

The day before your proposal presentation: prepare hand-outs foryour presentation (4 slides per page)

At the day of presentation: Set up Computer and Beamer (meet withsupervisor at 8:00 h am

Reviewer Group: ca. 1 week prior to the proposal date, meet withsupervisor and presenting group for a brief presentation of theproposal

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 thesupervisor (again to supervisor & R. Abele)

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 thegroup 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

([email protected])• 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“ ☺

Protein translocation into peroxisomes(Peter Mayerhofer)

12. 14.07.09

Chaperone-mediated autophagy: The way to survive starvation(Rupert Abele)

11. 07.07.09

Viral immune escape strategies(Andreas Hinz)

10. 30.06.09

Transmembrane communication within bacterial two-component systems(Roger Daheim)

9. 23.06.09

How do enveloped viruses enter into host cells?(Andreas Hinz)

8. 16.06.09

Intramembrane protein cleavage by the γ-secretase complex(Rupert Abele)

7. 9.06.09

Membrane insertion of tail anchored proteins(Robert Tampé)

6. 02.06.09

ABCE1 function in ribosome recycling(Robert Tampé)

5. 26.05.09

The macromolecular peptide loading complex(David Parcej)

4. 19.05.09

AAA-ATPase in protein unfolding (David Parcej)

3. 12.05.09

Reversible switchable fluorescent proteins: From optimization to application (Ralph Wieneke)

2. 05.05.09

siRNA Biology: From gene silencing to gene specific therapeutics(Katharina Ceh)

1. 28.04.09

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Introduction(Rupert Abele)

14.04.09

1. 1. siRNAsiRNA Biology: from gene silencing to geneBiology: from gene silencing to gene--specific therapeuticsspecific 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?


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11. 07.07.09


10. 30.06.09


9. 23.06.09


8. 16.06.09


7. 9.06.09


6. 02.06.09


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3. 12.05.09


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RecentlyRecently, , reversibly reversibly switchableswitchable fluorescent proteins (fluorescent proteins (RSFPsRSFPs)) havehave attractedattracted greatgreat attentionattention. . RSFPsRSFPs can can

switch between a nonswitch between a non‐‐fluorescent and a fluorescent state by fluorescent and a fluorescent state by lightirradiatinglightirradiating. This characteristic makes . This characteristic makes

them an ideal them an ideal flourophorflourophor with unique properties for optical labelling in an with unique properties for optical labelling in an spatiospatio‐‐temporal manner.temporal manner.

2. Reversible 2. Reversible switchableswitchable fluorescentfluorescent proteinsproteins


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3. AAA-ATPase in protein unfolding

Enzyme consuming ATP, that unfolds proteins, e.g. in the proteasome


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4. The Macromolecular Peptide Loading Complex


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5. ABCE1 function in ribosome recycling

• essential protein• involved in:translation initiationtranslation termination

ribosome biogenesisribosome recyclingHIV capsid assembly.


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6. Membrane insertion of tail anchored proteins

posttranslational membrane insertionC-terminal transmembrane helix

different pathways for insertion postulated


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?

7. Intramembrane protein cleavage by the γ-secretase

important event in the cleavage of APP to produce amyloid-β


12. 14.07.09


11. 07.07.09


10. 30.06.09


9. 23.06.09


8. 16.06.09


7. 9.06.09


6. 02.06.09


5. 26.05.09


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7. Membrane fusion

viral factors & SNAREs

How do enveloped viruses enter into host cells?


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5. 26.05.09


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9. Transmembrane communication within bacterial two‐component systems

Displacements of TMHs Rotation of TMHs


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10. Viral immune escape strategies

HIV glycoproteins & inhibition factors

What is the funtion of ......the glycan shield?...the hypervariability?...viral factors like Vpu?


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11. 07.07.09


10. 30.06.09


9. 23.06.09


8. 16.06.09


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6. 02.06.09


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11. Chaperone mediated autophagy

• lysosomal pathway to degrade long living cytosolic proteins• strongly induced under stress conditions


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11. 07.07.09


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12. Protein Translocation Into Peroxisomes

cytoplasmic polyribosomes

membrane proteins

matrix proteins

lipids

peroxisome

• Peroxisomal proteins areimported post-translationally

• The peroxisomal matrix protein import machinery accommodatesfully folded / oligomeric proteins

• Peroxisomal proteins are recognized byreceptors (e.g. PEX5) in the cytosol

Documents

Biochemistry III – Proposal seminar