NIH Mock Proposal    
1. Specific Aims    
2. Background and Significance    
3. Research Design and Methods    
4. References

This is a copy of a research proposal that I recently wrote to fulfill a qualifying exam requirement for my PhD program. I had to write a National Institutes of Health (NIH) style research proposal on a topic that is different from my thesis lab research, and then I had to present it to a committee of professors (called an oral defense!). I will eventually add explanatory comments throughout the presentation as it was written for professors who have some familiarity with the topic and research methods. Since the proposal is rather long for a single web page, I have subdivided it into sections. The most interesting parts for most people will be 1. Specific Aims and 2. Background and Significance. Section 3, Research Design and Methods, until I have time to annotate it, will be of most interest to those with a little background in the field and in research methods.

1. Specific Aims

The exact function of the protein involved in Friedreich ataxia (FRDA), an autosomal recessive neurodegenerative disorder, is unknown, and no treatment to prevent or slow disease progression exists. Elucidation of the function of the protein involved, frataxin, will aid in therapeutic intervention of disease progression. Yeast genetics with the homologous protein, YFH1, allows one to investigate the role of frataxin in cells and identify interacting proteins. Studies using YFH1 have already provided a clue as to the function of frataxin; it may play a role in regulation of iron levels in the mitochondria. Functional studies of frataxin could thus shed light on the cause of disease and on the as yet unidentified mitochondrial iron transport system.

1.1 Hypothesis

Deletion/underexpression of frataxin leads to iron accumulation in the mitochondria in both humans and in yeast. In yeast, loss of mitochondrial DNA, presumably due to oxidative stress because of high iron levels as the result of Fenton chemistry. This is also seen in deletion strains. Thus, frataxin may play a role in regulation of iron levels in the mitochondrial. The exact function of the protein; however, remains elusive, and the discovery of other interacting proteins may help to clarify if and how frataxin acts as an iron regulator. Since frataxin most likely plays a role in iron regulation, it is logical to see if it regulates mitochondrial iron transport genes. Specifically, frataxin may physically interact with the transporters and down-regulate iron influx into the mitochondria (Figure 1).

Possible targets of YFH1 could be two mitochondrial iron transporters (MFT1 and MFT2) recently discovered in yeast. A proposed model for iron regulation in the mitochondria is that MFT1 and/or MFT2 may be constitutively active in iron transport into the mitochondria. Frataxin could be a negative regulator, and a deletion in frataxin would then result in accumulation of iron to toxic levels. Overexpression of the MFT proteins would lead to higher levels of iron, but in the presence of frataxin, levels would not reach toxicity. If MFT1 and MFT2 act independently of frataxin; there are could be other as yet unidentified mitochondrial iron transporters, and thus other interactions need to be investigated.

1.2 Specific Aims

Proteins that interact with YFH1 will be identified using the genetic, biochemical, and molecular methods.

1. Yeast genetics will be used to test protein interactions between frataxin and MFT1/2.

2. Interacting proteins may also be identified biochemically by immunoprecipitation of mitochondrial protein extracts with an antibody to YFH1.

3. Additionally, a third molecular method employing the yeast two hybrid system will identify protein interactions.

Next Section: Background and Significance

You are visitor # since 1/12/99.