Exploring the Role of Hydrocarbons in Inducing Toxicity in Rainbow Trout

1. Biology 537 Writing an Effective Research Proposal DUE OCT 14 (worth 10%)

2. All research starts with a proposal, which is • an essential, and increasingly critical component of a request for support, usually funds, but may also be for equipment, personnel or access to research infrastructure (eg ship time for ocean studies, access to telescopes, synchrotrons) • usually up against stiff competition from other requests, because funds are very limited • read by only a few reviewers, both experts and (often) people with general backgrounds (so multiple audiences)

3. What makes a good research proposal? • Good idea convince others that you have a worthwhile research project • Clear hypothesis what are you testing/predictions? • Sound approach you have the competence and the work-plan to carry it out successfully

4. Well-written! Reviewers should • enjoy reading your proposal (be ruthless about writing, getting feedback, re-writing) • get excited about your question right away! • believe your plan is workable • find it easy to follow your argument, find all the details they need, and find NO errors Always be explicit - reviewers can’t mind read!

5. The very best proposals • explore novel ideas at the “cutting-edge” with creative, elegant tests • tackle important questions • persuade reviewers to “buy in” The clearest indicator of research quality is the extent to which it moves a field forward and stimulates work by others .

6. In a real competition • The applicant must have a first class track record on 3 fronts: i) contribution to science (publications) ii) expertise (or colleagues with expertise) iii) an excellent record of training (undergrads, grad students, postdocs*)NB reviewers are also influenced by previous success at obtaining funding!!

7. Why do we make you do a research proposal? • a critical step in organizing your thoughts and plans and thinking through the logic of what you intend to do • will your project result in clear conclusions at the end? will you know more about something important?Or will you be left with just a mass of data?

8. The 537 Proposal Guide (posted) Format (page counts are rough guides) 1. Background information (3/4 page) – Use the current literature to set the context for your research question. Show how your research question builds off the current literature. What is your hypothesis? Why is your hypothesis important? How will your research fill gaps in the field? Why is the work significant? 2. Plan of Research (2 pages) – What are the aims of your research? For each aim: (i) State the hypothesis clearly. (ii) Present a rationale for the aim. (iii) Describe the experimental approach and why this is the best approach? (iv) Identify the potential problems and alternate approaches. (v) State the anticipated results and interpretation. 3. Expected significance (1/4 page) – Why is the research important?

9. Think about your TITLE • Does it capture your thesis problem? • Is it interesting? • Is it concise? which is better…… “The role of hydrocarbons as agents of toxicity in rainbow trout exposed to excess heavy fuel oil” OR “Do hydrocarbons induce toxicity in trout following a fuel oil spill? ”

10. The title you provide will be what is advertised on the Seminar Schedule

11. SECTION 1: Background section – 3/4 page • Describe the current state of the field with details relevant to your proposal – set the context for your exciting question • How will your proposal move the field forward? (don’t just say you are “filling a gap”) • Why is your research significant? • Common mistakes -irrelevant details -missing relevant information

12. Go that extra step….. • Show how your idea builds off the current state of knowledge • Point out how the current research supports your hypothesis – this will, in turn, show you know the idea is feasible AND you know what technical expertise is required

13. The role of the Literature Search* • Ensures that you are not "reinventing the wheel". • Gives credit to those who have laid the groundwork for your research. • Demonstrates your understanding of the theoretical and research issues related to your research question. • Shows your ability to critically evaluate relevant literature, integrate and synthesize essential background. • Provides new insights or develops a new model as the conceptual framework for your research. • Convinces your reader that your proposed research will make a significant and substantial contribution to the literature (e.g., resolving an important theoretical issue or providing important new data).

14. Bad literature reviews • Lacking organization and structure • Lacking focus, unity and coherence • Being repetitive and verbose • Failing to cite influential papers • Failing to keep up with recent developments • Failing to critically evaluate cited papers • Citing irrelevant or trivial references • Depending too much on review articles!

15. Really bad literature reviews! • Failing to use literature relevant to your question! • Cramming in too much detail • Do not give a listing of papers with short summaries of each. A document that says "paper 1 has done this, paper 2 has done the other" makes for a very poor survey. • Copying material from papers without attribution = plagiarism

16. Framing the research proposal • Clear statement of question and hypothesis • State your rationale… I hypothesize that …. This will be tested in Aim X • OR: In this study, I will test the following hypotheses (see Section B.7 of the Thesis Writing and Formatting Guidelines)

17. The hypothesis ! • If you write an introduction with impact, this will lead to the formulation of your hypothesis. • A well-written hypothesis can be summed up in one phrase. • A strong hypothesis generates testable predictions • See additional information in Thesis Writing and Formatting Guidelines

18. Hypothesis example • Higher exposure to UV rays will lead to increased incidence of skin cancer = Prediction! • Ultraviolet light exposure causes skin cancer= Conclusion! • Ultraviolet light exposure may cause skin cancer = A hypothesis – but not a good one! • Skin cancer is caused by UV damage to DNA. If so, people with a higher exposure to UV light will have a higher frequency of skin cancer. =Formalized hypothesiswith testable prediction ✔

19. YOUR THESIS MAY FOCUS ON Developing an approach or Identifying a key mechanism CONSIDER USING A DIAGRAM or FLOW CHART TO FRAME YOUR HYPOTHESIS STROKE Energetic compromise in penumbra PIDs in vulnerable tissue Loss of ion homeostasis INCREASING NEURON DEATH Figure 8. Diagram illustrating the objectives of the research. Using repetitive anoxia to model PIDs in a system that allows rapid and reliable molecular genetic investigations, Objective 1 will discover ways to suppress PIDs which cause the irreversible loss of ion homeostasis leading to increasing brain damage. Objective 2 will characterize how PIDs are generated so that therapeutic strategies can be devised. X OBJECTIVE 2 X OBJECTIVE 1

20. BUT NOT ONE LIKE THIS! Drostar 1, 2 (Adults) Farnesoic Acid o-MethylTransferase - (FA) Epoxidase (MT) (ED) 10,11-epoxy FA Methyl Farnesoate ED - (JH III Acid) (MF) 6,7-epoxy FA ED ED Drome-PISCF Adult ED ED Bisepoxy FA MT - 6,7-epoxy MF (JH III) sNPFR, NPF-R + ED + + ED MT NepYr, NPF larvae + Drostar 2 (larvae) Bisepoxy JH III + NepYr Adult (JHB3) + Drostar 1 (larvae)

21. Knitting the Background with your Hypothesis • Spell it out…. “Previous work has shown A Recent work has shown B My hypothesis/model suggests C..” • State why it’s important…. “If C is true, then we have…..” OR “If completed, the impact would be…..”

22. SECTION 2: Research Plan & Methods (2 pages) Aims and Objectives The aim is what you want to achieve, and the objective describes how you are going to achieve that aim • each aim should focus on one question (there can be multiple approaches to each aim) • make sure that each aim is matched with specific objectives • limit the number of aims in your proposal – 3 maximum

23. One idea per aimFrom Dr. Hawryshyn Aim 1) Test the hypothesis – ultraviolet cone photoreceptors disappear from the retina in salmonid fishes Based on our observations that the geometry of the cone mosaic changes I propose to: 1.1 Characterize the changes in the cone mosaic using immunohistochemistry 1.2 Measure changes in ultraviolet photosensitivity electrophysiologically. 1.3 Test the hypothesis that UV cones disappear from the retina by identifying cones that are co-labeled with UV cone Ab and Tunnel Ab.

24. Framing the research proposal cont’d • Outline experimental approach (use subsections as necessary) • Describe your anticipated results and interpretation • Identify potential problems and alternatives

25. SECTION 3: Expected significance – ¼ page Once again, why this is important??? • If my hypothesis is proven correct, this provides a • new insight … • new generation of treatments… • basis for the next study of….

26. Fatal errors • Over-proposing – too many aims and unrealistic scale of project • Too many “fishing trips” – looking at too many responses for a single aim (can’t see the forest for the trees) • Aims built on success of previous aim – where’s the backup plan? • Too much detail in Methods

27. How to avoid fatal errors: Pay close attention to your writing! (See Section C of the Thesis Writing and Formatting Guidelines for helpful tips and Resources) • Monitor your SPELL CHECKER • Make sure the grammar is correct • Make sure that you are communicating your ideas clearly. Just because you understand what you have written does not mean that someone else will understand! • Grammatically correct ≠ clearly presented ideas • Pay attention to your phraseology and jargon • Paragraphs can be a good thing (leave white space)

28. Delete redundant words • ultimate outcome • young juvenile • period of time • combine together • each and every • reduce down • separate out • most unique • differentspecies • repeat again • combine into one • absolutely essential Recent studies by Bendena and colleagues have shown that … becomes … (Bendena, 1967) Previous work has shown … becomes …

29. Proofread! • Delete unnecessary words (from Learning to Write Biology) • As you know… (if readers know ..why re-tell) • Needless to say… (if needless don’t say it!) • I might add that… (just add it) • It is important to note here… (is other material unimportant!) • When time permits… (sounds poetic but inaccurate!) • As already stated… (if you said it why say it again!) • Quite similar or looks similar

30. Use active voice • This is an important area of research … • The current state of knowledge in the field is … • There is an unresolved problem which needs to be answered ... • Because … • I have an IDEA … • The best way to test this idea is … • Because … • To test this idea I will perform the following experiments and analysis: I will make these measures … The techniques will work because … I am aware of these potential confounds … I will take these precautions… My criteria for judging if something has happened are … • The results will be significant because …

31. Format and Marking Criteria First page should contain the study title and the names of the supervisor (and cosupervisor if relevant), and the committee member*. The main text should be on Pages 2 to 4 (3 text pages MAX), double-spaced, 12pt font, 2.5 cm margins all round (Reference list and Figures separate i.e. not included in page count). Figures optional. *This information is REQUIRED in order to schedule your seminars • Quality of writing and clarity of the proposed research – 3/10 points • Logical development and organization of proposal – 3/10 points • Feasibility of proposed research – 2/10 points • Significance of the proposed research – 2/10 points N.B. It is primarily the quality of the writing that is being marked … not the science details

32. Research Proposal submission Put a stapled hard copy (printed on both sides of the page) in Grogan mail box outside Biology General Office (Bioscience 3rd floor) before 3.30pm on Friday October 14th. AND e-mail Microsoft WORD version to groganp@queensu.ca (Both hardcopy AND electronic versions are REQUIRED by that date and time)

33. Resources: NSERC