BIOL256 Experimental Genetic Analysis
Fall 2005



To use your understanding of experimental genetic analysis to design a genetic approach to a question of interest, and to expose you to model genetic organisms and genetic systems in addition to Arabidopsis.

General instructions

Proposals can address any biological question, as long as it is not addressed using Arabidopsis. The proposal should present the objectives of the proposed work, and the suitability of the genetic methods to be employed. It should present the merits of the proposed project clearly and should be prepared with the care and thoroughness of a paper submitted for publication. Sufficient information should be provided so that readers will be able to evaluate the proposal in accordance with the following review criteria:

(1) Background:
Did the applicant adequately consider previous work in the field?

Is the choice of system/organism appropriate for the question?

(2) Approach:
Are the conceptual framework, design, methods, and analyses adequately developed, well integrated, and appropriate to the aims of the project?

Does the applicant acknowledge potential problem areas and consider alternative tactics?


Preliminary proposals are due 11/11/05 by 5 p.m.  Final written proposals are due 12/19/05 at noon.

Preliminary Proposals

Getting started: Make a list of questions or phenomena that interest you. If there is a particular question that has always intrigued you, I encourage you to focus on it. I hope that you will realize that many questions can be addressed using one or more of the genetic approaches we've discussed in class this semester. Once you have one or more potential questions in mind, use a combination of the websites below and available literature to determine which organism would be best suited for your project. If your question is too broad to answer with a single organism, you should either 1) narrow your question or 2) propose to use one organism as a pilot study that would help you begin answering your larger question. I have made this constraint in order to prevent your project proposal from becoming too enormous! (i.e. I think/hope this is for your own good, even though it is a limitation)

Writing your preliminary proposal: Your preliminary proposal should include the following:

1. A project title that is brief, yet represents the major thrust of your project. Highly technical words and phrases should be avoided. Do not use phrases such as "investigation of" or "research on".
2. A statement of the biological question to be addressed.

3. A statement justifying the choice of organism.

4. A statement of the specific genetic approach to be employed, and the justification of using this approach to ask your question.

5. An annotated list of relevant literature (at a minimum, 2 primary sources and 1 secondary source). This should include  a brief (two to three sentence) summary of the major points of each of these sources.

Formatting: Your preliminary project proposal should be about 2 pages of text (12 point font, 1.5 - 2 line spacing, 1 inch margins). You are expected to proofread your proposal before submission. I will return (ungraded) any proposals that require substantial proofreading, and late penalties will apply to proposals returned due to a lack of proofreading.

Final Proposals

Getting started: Your goal here is to expand on your preliminary proposal. The section that will require the most expansion is that of your experimental approach (this is the same as the research design, number 3 below). My recommendation is to "map out" your experimental approach. You might try using a flow chart, in order to pin down the areas that need to be filled in (but such a flow chart should not be included in your final proposal). As stated below, this section should include enough detail that your reader can clearly and completely understand the approach you are proposing to take.

Writing your final proposal: Your final proposal should include an elaboration of each parts of the preliminary proposal. In addition,  it should include:

1. An introduction, including the purpose of the project (i.e. the central question).
          2. A background section that puts your question (and proposed project) in perspective in relation to the current literature.
3. Your research design, which is the major section of the proposal. This should include sufficient detail that the reader can clearly and completely understand the experiments you propose to undertake, the rationale behind proposing these particular experiments, and the results you expect to obtain from these experiments. In addition, this section should address the potential problems you might encounter in taking this approach, and alternative tactics that could be employed if you were to encounter these problems.

For example, if you are proposing a genetic screen, this section should include mutagen concentrations (as well as the rationale for thesse concentrations), the number of organisms to screen (and why), how many mutants you expect to identify (again, should include rationale), how you will characterize the mutants identified, etc.

If you are proposing to use a TILLinG screen, this section should include an explanation of how you would create mutations, the gene to be studied including the specific primers to be employed, a description of the analysis (you may not say that you are going to ask a center to do it for you (this is true for any case)), the types of phenotypes you  expect (and why), how you will characterize the mutants identified, etc.

Of course, I have only included two examples above, and there are many other genetic approaches that one could employ (quantititative trait analysis, mapping and positional cloning of a gene based on previously isolated mutations, etc.)

4. A section on future directions that you would take having accomplished your proposed project. Discuss the types of questions you would ask next and (briefly, no experimental details necessary here) how you would go about this.

Formatting: Your project proposal should be 8 -10 pages of text (12 point font, 1.5 - 2 line spacing, 1 inch margins). References and figures will not be counted within the page limit. If you are including figures, they must be computer generated. You are expected to edit and proofread your proposal before submission. I will return (ungraded) any proposals that require substantial proofreading, and late penalties will apply to proposals returned due to a lack of proofreading.

Useful links


WormBase A Worm Image


The Whole Mouse Catalog 


  Dictyostelium discoideum

Gramene: A Comparative Mapping Resource for Grains


last updated 082905