Current Topics in Genes and Development

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Current Topics in Genes and Development Spring
2007 Scientific Writing Sharon Dent Greg May
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Most Research Proposals have these
elements Title Abstract (350 words or
less) Specific Aims (1 page) Background and
Significance (3 pages) Research Design and
Methods References
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From GSBS Website It is the students
responsibility to submit a Research Plan in the
form of a research grant proposal Title Abstract
(350 words or less) Specific Aims Background and
Significance Research Design and
Methods References

DENT

MAY
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References GSBS Web Site http//gsbs.uth.tmc
.edu/policies/proposal.html MDACC Scientific
Publications Dept http//inside.mdanderson.org/d
epartments/scipub
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Title self-explanatory should describe scope
of work active is better than passive Examples
Definition of histone acetyltransferase
functions during Mammalian Development vs. Analy
sis of HAT expression and characterization
of phenotype of HAT knock out
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Abstract introduces reviewers (faculty) to the
grant should emphasize hypothesis to be tested,
significance of research, and specific
goals
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• Example abstract 1
• The sequence of p106 is very similar to that of
  p53,
• but the functions of p106 are not known.
  Experiments in this
• proposal will test the hypothesis that p106 is
  important to
• cell cycle progression. Three specific aims are
  proposed
• to disrupt the p106 gene in mice 2) to do siRNA
  experiments
• in cell culture and 3) to over express p106 in
  cell culture.
• These studies will increase our understanding of
  cell
• cycle control and cancer formation.

What is good about this abstract? What is
lacking?
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Example abstract revised Set the stage
Mutations in the tumor suppressor p53 are
associated with more than 50 of all human
cancers. p53 is known to play an important role
in controlling cell cycle progression and in
determining whether or not a cell undergoes
apoptosis. Recently, a gene very similar to p53
in sequence, p106, was discovered. Provide
rationale for hypothesis Like p53, the p106
gene is expressed ubiquitously and is located in
the cell nucleus. Preliminary studies indicate
that p106 expression is down regulated in
transformed cells in culture. Experiments in
this proposal will test the hypothesis that p106
has functions similar to those of p53 in
controlling cell cycle progression and cell
survival.
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Describe aims Specific aims include 1)
Determining the effects of loss of p106
expression on cell growth and transformation
using gene knock out approaches in mice and
siRNA experiments in tissue culture. 2) Defining
the effects of overexpression of p106 on cell
growth and tumor formation in transgenic mice
and 3) Determining the frequency of p106
mutation in breast and ovarian tumors. Stress
significance and long term potential Long term
experiments will define the locations and
functional consequences of any tumor-associated
mutations in p106. In addition, these studies
will provide a platform for future studies
directed at understanding the coordination of
the functions of p53 and p53-related proteins
such as p106. Collectively, these studies will
provide important and novel insights to both
normal controls of the cell cycle and to
abnormalities in these controls that lead to
cancer.
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SPECIFIC AIMS
One page description of the goals of the
proposal Often the most important page in the
proposal never get a second chance to make a
first impression
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• Specific Aims Page should
• Provide description of the state of the field
• and gaps in knowledge. Also should describe
  system
• to be used and novelty or appropriateness
• of the system.
• Provide rationale for hypothesis and
• clearly state the hypothesis.
• Describe each aim of the grant in terms of
• questions that will be answered or information to
• be gained. (NOT just a list of experiments!)
• 4. Provide info on technical approaches but these
• should be not be the focus of the aims.
• 5. Should end with big picture significance
• and long term potentials

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• Each Aim should
• Be active, not passive.
• ie, use goal oriented verbs
• determine, discover, elucidate
• much better than
• study, analyze, measure
• Be independent.
• If one aim fails, others should still be
  feasible
• and important
• 3. Be hypothesis driven, not technique driven

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For GSBS Proposals, Abstract and Specific aims
can be combined into one page 1. Abstract at
top to set stage for the aims 2. Followed by
listing of aims 3. End with summary of
significance and potential
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What is good/bad about these aims??
   1). To develop an in vitro transcription
system to measure VIG1 expression in the
presence and absence of MFG.      2) To use the
in vitro system to define what domains in
MFG are required for VIG1 activation. 3) To
introduce mutant versions of MFG that do not
activate VIG1 (as defined above) into transgenic
mice and characterize their phenotype.
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• Revised Aims
• Determine if MFG can directly stimulate VIG1
• transcription using a highly defined in vitro
• transcription system. These experiments
• will determine if MFG can activate VIG1 on its
  own
• or whether additional cofactors are required.
• Elucidate the importance of MFG toVIG1 activation
• in vivo. Transfection of cultured cells and
  mouse gene
• targeting or transgenic approaches will be used
• to determine if increasing or decreasing
• MFG dosage impacts VIG1 expression.
• Define domains in MFG or associated cofactors
• involved in regulation of VIG1 via mutagenesis.
• These experiments will provided insights to the
  molecular
• basis of MFG functions.

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Putting it all together
Abstract and Specific Aims   VIG1 is a Very
Important Gene that mediates a variety of
developmental signals. Mutations in VIG1 have
drastic effects on cell-cell communication
during development in flies, leading to early
embryo lethality. Although much information has
been gained in the past few years regarding VIG
functions, the factors that regulate this gene
have been difficult to identify. These factors
are themselves likely to be very important to
normal fly development. Recently, I discovered
a mutation in flies that results in very low VIG
expression levels. I succeeded in cloning the
wild type version of the gene that was mutated
in these flies. The sequence of this gene,
which I have named My Favorite Gene (MFG), has
many hallmark features of a transcription
factor, including a Zn-finger type DNA binding
domain and a domain with sequence homology to
the activation domain of the strong VP16
transcriptional activator. Based on these
findings, I propose the hypothesis that MFG is a
direct activator of VIG gene expression. The
following Specific Aims are proposed to test this
hypothesis  
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• Determine if MFG can directly stimulate VIG1
  transcription
• using a highly defined in vitro transcription
  system.
• These experiments will determine if MFG is a
  transcription factor that can activate
• VIG1 on its own or whether additional cofactors
  are required.
• Elucidate the importance of MFG toVIG1 activation
  in vivo.
• Transfection of cultured cells and gene targeting
  or transgenic approaches
• will be used to determine if increasing or
  decreasing MFG dosage impacts
• VIG1 expression.
• Define domains in MFG or associated cofactors
  involved in regulation
• of VIG1 via mutagenesis. These experiments will
  provided insights
• to the molecular basis of MFG functions.
•  
• Collectively these experiments will define the
  molecular functions of MFG
• and its role in VIG1 regulation. They will set
  the stage for additional
• studies to identify additional factors involved
  in controlling VIG gene
• expression and the cis-acting DNA elements
  required for VIG regulation.
• In the long term, these studies will provide new
  insights to the molecular