Purpose: Writing proposals for research funding is an essential skill in science. Your final assessment for BIOL 309 will be a research proposal that builds on the work you have done throughout the semester. A successful research proposal summarizes the state of knowledge in the field, presents some original preliminary research, and suggests promising avenues for future research that will fill a gap in current understanding.
Instructions:
Your proposal should be no more than ten pages double spaced (not including the title page), including references and figures, 12-point Times New Roman or 11-point Ariel font.
You can submit your proposal as a Word document or PDF.
You should reference at least ten references. These references can be peer reviewed primary research papers or review papers. Only cite relevant papers that contribute to your understanding of Hydra biology, bioinformatics, and secreted proteins. Note that all papers you cite do not have to be about Hydra! Some could be about related organisms or secreted proteins from the same family as the one you worked on.
Start by outlining your proposal. Identify the protein or protein family you will be focusing on, the experiments you want to propose, and make a clear statement of your hypothesis.
Your proposal should have a clear narrative structure, starting with what is already known in the field, identifying a gap in current knowledge, progressing to your preliminary research, and finally to your proposal for how to fill the gap in current knowledge.
Keep your intended audience in mind: fellow biology majors who may not have any background in the specific area of your research.
Your research proposal may include tables, charts, images, and diagrams, and these count toward your total pages.
Your paper should contain the following sections:
Cover page: With title, date, your name, class, and section.
Background: (2-3 pages). Introduce the topic. Summarize the state of knowledge in the field, providing references to primary research papers and relevant reviews. Identify the gap in knowledge that your research will address.
Preliminary data (2 pages): summarize bioinformatics data you have collected during the semester and how it informs your research proposal.
Hypothesis: clear statement of testable prediction. This can be at the end of your preliminary data section.
Experimental proposal (4 pages): Briefly outline the experiments you will perform, the data you will collect from these experiments, and how that data will be analyzed. These can be techniques we have learned about in class or techniques you have read about. Include how the results of each experiment will help address your hypothesis.
Conclusion (1 page): summarize gap in knowledge that you intend to fill with the proposed research, main points of preliminary data, your hypothesis, main experiments proposed and expected results of those experiments.
Specific suggestions:
Pick your protein: your BLAST search should give you a clue to its function and the single cell transcriptome data should give you a club to where it’s expressed. Choose a protein you are intrigued by and design experiments to learn more about its function and expression patterns.
Your background should include why in general we are interested in studying secreted proteins in Hydra, and anything that is already known about the protein or protein family you have decided to study. This can be from Hydra or from other organisms. For example, if your BLAST search turned up that your protein is a metalloproteinase, you might want to tell us what a metalloproteinase is, what is known about its function in other organisms, and what is known about its function in Hydra.
Your preliminary data can include:
How do you know this is a secreted protein? How long is the signal sequence and where is the predicted cleavage site? You can run SignalP again on just your protein to get the data and graphs.
Is this a transmembrane protein? If so, how many transmembrane segments are there? Are there any other notable features of the protein, like a long extracellular or cytoplasmic domain? You can run the transmembrane server to get the hydrophobicity plot for just that protein.
What are the top BLAST hits for your protein and what do they tell you about the protein’s function? Does it have any conserved domains? (You can find this by scrolling down to the PFam section of the gene page on the Hydra genome server.)
Is it differentially expressed? Which cell types is it likely expressed in? You can download images from the single cell server (scatter plots, bar plots or violin plots).
Your experiments should focus on the localization and/or the function of the protein you have selected. We will cover several common techniques for addressing these questions in class, but you can also include techniques you have read about in papers even if we have not covered them in class.
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