FMHS-CSCR Research Workshop 2012

23 April, 2012 (Monday, 2.15-2.40 pm)

Writing a research proposal

Professor Choo Kong Bung

Faculty of Medicine and Health Science

Universiti Tunku Abdul Rahman
Sungai Long, Kajang
Selangor

Email: chookb@utar.edu.my;
Office: K301 (3rd floor)
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Why write research proposals?

** To obtain funds to support our research

** To review and to establish further focus(es)
of ongoing research programmes
** To develop novel ideas during writing of
proposal
 Preparation
Decide on the granting body
Clarify qualification of applicants
Know the application procedure, time open for
application & obtain all application forms
Is it a group or personal project?
Collaborators: co-PIs or associate PIs??
 Understand the culture
of the granting body
& the application procedure
 Different types of research proposals

e.g. Ministry of Higher Education (MoHE)

FRGS: Fundamental Research Grant Scheme

ERGS: Exploratory Research Grant Scheme

LRGS: Long-term Research Grant Scheme

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 Long-term research grant

** May need to first submit a concept paper

** PI and team members may be asked to present

the proposal orally

** Writing up of a full proposal for further review

 Principal Investigator (PI), co-Principal
Investigator (co-PI) or Associate Investigator

PI: should have the relevant background/experiences

to supervise and execute main body of the project
Co- and associate PI should have relevant expertise
and experiences to complement the PI
 Major issues to be addressed
in a research proposal
Goal What is our objective?
Significance
Why is the project important?
Design / approaches How to achieve the goal ?
PI & co-PIs
Who are doing which part of the study ?
For multi-year project
When is each specific aim
expected to be achieved ?
Impact of project When the project is successfully
carried out, so what ?
Forecasts based on project data What next ?
Keys to good proposal writing
** Clear and concise
(good command of language )

** Evidence-based & logical

(avoid wild speculation )

** Relevance
(avoid unnecessary information )

Be reviewer friendly!!
Content of a successful research proposal

** Addressing interesting & worthy questions/issues

** Clear and innovative concept and rationale

** Achievable aims

** Appropriate experimental designs with feasible

and up-to-date techniques

** Interesting and convincing preliminary data

or relevant previous publications

** Competence and publication record of PI

Always have a rational
and achievable goal!!
 Preparing and writing up a research proposal
Preliminary Observations

Preparation
Results

Literature
Review Questions

Hypothesis

Goal & aims

Writing up

Experimental design

Anticipated problems
/Expected results
 Hypothesis
Use relevant literature and preliminary data to
build the hypothesis

Use diagrams to outline ideas and models

State the hypothesis clearly in the abstract and
specific aims
 A roadmap of the project
Display the various steps on how the various
specific aims are integrated

Reveal the major experimental design and

methods to be used (e.g. real-time PCR, microarray,
bioinformatics, knockout mice ..)

Show timeline (milestone on completion of each

specific aim over the granting period)
 Transcriptional regulation of Zfp352 (Yrs 2-3)
Specific aim 3
Overall scheme:
Upstream regulator gene(s)
An example
Upstream Specific aim 2 Effects of Zfp352 knockdown on development (Yr 2)
regulator siRNA k/d
Effects on development

Zfp352 regulation
cis ZFP352 gene

ZFP352
Specific aim 4
ZFP352 interaction proteins & PTM (Yr 3)
associating ZFP352 Preimplantation
protein(s)
protein development

PTM

Activation of downstream
target genes
C(A/T)CCC
Target gene(s)

ZFP352-binding site(s)

Specific aim 1 Identification of X Y Z
downstream target genes (Yrs 1-2) ZFP352-regulated d/s protein(s)
 Experimental/study design
** Study design is NOT Materials and Methods

** Design experiments to address the questions

raised in the specific aims

** Be realistic, manageable and focussed

** Be logical in step-by-step leading to your goal

 Be reviewer friendly
Present information logically, concisely & clearly
Make appropriate sections and subsections with
concise & informative titles and subtitles under a
logical numbering system
Prepare a list of content with page numbers of sections
and subsections
The following important sections are definitely read
very carefully by the reviewers, so write well: specific
aims, study design approaches and integration.
Writing up the proposal
The basic structure of a research proposal (I)
1. Title
2. Abstract
3. Specific aims
4. Background/literature review
& significance of project
5. Preliminary data
6. Study design and major approaches
7. Materials and methods
The basic structure of a research proposal (II)
8. Anticipated results
9. Anticipated problems & solutions
10. Literature cited
11. Biodata of PI and collaborators
12. Research environment and supports
13. Budget
14. Approval from Ethics Committees
15. Appendices
 Title of a research proposal
Should clearly reflect the major goal of the proposed
research
Concise, informative and attractive
Create a title by first making a list of keywords
Avoid acronyms
Should be decided on when the proposal is finalised
 Abstract
Most important section; will be read closely by
reviewers (First impression on the reviewers)
Final section to be written (or prepare an early draft
but finalised last )
Be concise, comprehensive and organised
(beware of word limitation )

Should include all key points of whole proposal:

Background, hypothesis, specific aims, study design,
significance of study & anticipated results
 Abstract: an example
Importance Early onset breast cancer has been the unique and major health
problem in Malaysia with annual increase of

Outstanding The etiology and mechanisms of breast cancer in young

problems women is unknown. It has been suggested that carcinogenesis
in utero may account for the early-onset of this cancer

To test this hypothesis, we have used fed pregnant mice with

Hypothesis fatty diet and found increase in incidence of mammary tumours
in the new born mice
In this proposal, we will examine the alteration of mammary
Experimental gland differentiation pathway in the mammary tumours derived
approaches from the new born mice using microarray, SAGE (serial analysis
of gene expression) as well real-time PCR techniques
This study of alterations in mammary gland differentiation in the
Summary mammary tumour of new born mice will allow us to identify the
Answers genetic and molecular mechanisms involved in the early-onset
breast cancer.

This information could be useful for diagnosis/treatment of

Significance
early-onset breast cancer in Malaysia
 Goals and specific aims
What do we intend to achieve?
Goal(s): Overall and long-term
(best to have only one major goal)

Specific aims: milestones/steps to reach the goal

(no more than 3-5 specific aims)

Specific aims: Be specific, be achievable, be logical

>> Both goals and specific aims:

Clear link to test of hypothesis
Clear link to study design
 Specific aim: an example
Approaches Rationale and hypothesis

Specific Aim 1. To determine the role of nucleosomes in

the regulation of Igk locus rearrangement.
Our preliminary results showed that the V(D)J recombinase could
not recognize RSS targets if they were arranged into a
nucleosome structure. We propose experiments to extend
these observations by 1) determining what fraction of the Jk
gene segments are in the nucleosomal structure in cells
undergoing rearrangement as compared with non-lymphoid
cells, 2) determining if nucleosomes are phased across the
Jk locus, 3)determining whether nucleosome remodeling
complex can alter the accessibility of the Jk cluster in native
or reconstituted chromatin. This analysis will give us insight
of the mechanism of Igk gene rearrangement.

Significance
 Background and significance
WHY the study is important?
Describe what has or has not been reported (current
status of information)
Importance of the research goals & potential benefits
derived from the study
Cite relevant and up-to-date literature
Consider the pros and cons of the subject matter
Demonstrate that we are fully qualified & competent
to address the stated questions
This is not writing a review; limit to 3-5 pages
 Preliminary data
What are the pilot studies have we done?

Describe only relevant preliminary data

Describe how the hypothesis is developed from and

supported by the preliminary data

Figures & tables should include legends & footnotes

(as in writing up a research paper)
Limit to 2-4 pages (including figures and tables)
Study design & experimental approaches
HOW do we plan to execute the project?
Rationale of study design and major techniques to be
used
Variables and parameters of the major exptl
approaches

Study design & methods must be feasible & integrated,

and be consistent with specific aims and goal
Potential pitfalls and alternative strategies when
problems are encountered
Study design & experimental approaches

This section should include an integrated scheme

(roadmap) of the core steps of the proposal

Describe how experiments are to be done; more

importantly, also explain why

Also need to cite appropriate supporting literature

Limit to 4-6 pages

 Transcriptional regulation of Zfp352 (Yrs 2-3)
Specific aim 3
Overall scheme:
Upstream regulator gene(s)
An example
Upstream Specific aim 2 Effects of Zfp352 knockdown on development (Yr 2)
regulator siRNA k/d
Effects on development

Zfp352 regulation
cis ZFP352 gene

ZFP352
Specific aim 4
ZFP352 interaction proteins & PTM (Yr 3)
associating ZFP352 Preimplantation
protein(s)
protein development

PTM

Activation of downstream
target genes
C(A/T)CCC
Target gene(s)

ZFP352-binding site(s)

Specific aim 1 Identification of X Y Z
downstream target genes (Yrs 1-2) ZFP352-regulated d/s protein(s)
From Choo KB
 Literature cited
Literature cited must be appropriate, complete and
up-to-date

Best to list the full title of each cited paper besides

authorship and journal source

Check to make sure of the correctness of cited papers

Restrict to 40-60 most important papers

 Biodata of PI and co-PI

Use only updated biodata

Include publications in the past 5 years
May also include conference abstracts and
monographs and books published
Research environment & support
Is the research environment of the PI equipped to
successfully carry out project?
(Emphasis on superior research environment
e.g. core facilities, animal facilities )

Other senior or experienced collaborators in own

and other institutions
Supports from affiliated organisation of PI and co-
PIs

Availability of postgraduate students

 Budget
Know the budget ceiling & average budget range
Be reasonable; justify request of large sum
The budget may include
>Salaries (full- or part-time RA, postgraduate scheme)
>Instruments and software (with limitation)
>Consumbles (reagents, chemicals, plasticware )
>Others (conferences, MS handling fee, publication costs )
 Approval from
Research Ethics Committees

For use of human subjects: Internal Review Board

(IRB) or Ethical Committee
For use of animals: Animals Use & Care Committee
Recombinant DNA Research Committee
Best to submit for internal committee approvals early
to avoid delays in final submission
 Appendices

May include pdf copies of important supporting

papers, accepted or submitted manuscripts
Intellectual properties (IPs) or licensing
Agreement for use of expensive instruments from
other institutions
All other helpful supporting documents
Writing up a research proposal: summary

Completion and
submission of proposal

Write up, discuss, review and rewrite

Organise ideas, literature review, study design and

integration of specific aims into a roadmap

Decide on funding body; familiarise with application procedure

 A reminder
Absolutely
NO
PLAGIARISM!!!
PLAGIARISM in any published writing
is a MOST SERIOUS offence
 Some useful websites
http://www.nsf.gov/home/programs/guide.htm
http://grants1.nih.gov/grants/grant_tips.htm
http://www.niaid.nih.gov/ncn/grants/
http://deainfo.nci.nih.gov/extra/extdocs/gntapp.htm
http://cpmcnet.columbia.edu/research/writing.htm
http://www.csr.nih.gov/
http://www.grantcentral.com
 Best of luck
&
Enjoy our research

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