20.109(F09):DNA engineering "Progress Report"

Research projects take considerable time to complete, and "progress reports" are a common written form that has developed so others can evaluate intermediate stages of a larger, long-term project. Graduate students write progress reports for their thesis committees. Principle investigators write progress reports for funding agencies to summarize the ongoing successes and difficulties within a funded project. For this assignment, you will submit a progress report that describes the construction of the delta5 plasmid. You should write this report as if you were a 3rd year graduate student and you were submitting the report to your thesis advisory committee in advance of a meeting with them. You can presume they know the overall direction of your project from your first meeting with them and your qualifying exams, but now they would like to hear what progress you've made in the lab over the last few months. The following guidelines have been adapted for you from the requirements for Harvard's Division of Medical Sciences PhD Program.

Submission: October 6th or 7th, 2009
This assignment is due by 11:00 a.m. on the day you have lab. Please turn in your progress reports electronically by uploading them to the Stellar website that is associated with our class. It is important that you name your files according to this convention: Firstinitial_Lastname_LabSection_Mod1.doc, for example: S_Hockfield_TR_Mod1.doc

There will be a 1/3 letter grade penalty for each day (24 hour period) late. If you are submitting your assignment after the due date, it must be emailed to nlerner, lsutliff, nkuldell and astachow AT mit DOT edu. There will be no re-write option on this assignment.

The rubric used for grading your progress report is [[Media:Progress Report Rubric.pdf| here.]]

Cover Sheet
Your progress report cover sheet should include the title of your project, your name, the name of your collaborator (i.e. lab partner), your e-mail address, your advisor's name (i.e. instructors), an indication if this is the initial or a follow-up advisory meeting, the date.

Body of Progress Report

 * Background and Significance: A concise (i.e. one paragraph) review of the scientific premise that is relevant to the proposal, with emphasis on critical knowledge gaps likely to be filled by the proposed research.
 * Specific Aims: Overall goals of the research project. This section should take the form of a numbered list with no more than 2 sentences to describe each Specific Aim. At least 3 and no more than 5 Aims should be listed.
 * Studies and Preliminary Results: The studies directed toward specific aims and the positive and negative results obtained should be presented, as well as any technical problems encountered and how addressed. This section will be the longest of your Progress Report. It should refer to your lab data that will be attached as an appendix to the progress report.
 * Plans: A concise (i.e. one paragraph) summary of plans to address the remaining Specific Aims, including any important modifications to the original plans based on preliminary results.

Appendix to Progress Report
NOTE: if your own data did not result in the expected outcomes you should still include it here but ALSO include the sample data that's been posted to the wiki "talk" pages so you can illustrate your understanding of the results there too.


 * Figure 1: HR figure
 * You are welcomed to add additional figures to clarify the summary. Hand drawn figures are encouraged (but they would need to be scanned in order to email them as part of your report). You can use the figure that's used in lecture, but you must redraw it and also cite a primary journal or text reference for the information (not "Engelward lectures, 2009"). You can use published figures, but if you do so, you must include the reference to the published work. Reference format requirements are described in  the general guidelines for writing up up your research. Figures you use should not be downloaded from a web site.
 * Figure 2: Diagram showing what you did. There are two parts to this figure, one general and one more specific. Part A of this figure should offer a high level diagram for how the plasmids can be used to detect homologous recombination in mammalian cells. The reader needs to know what the goal is: which plasmid did you set out to create? Part B of this figure would ideally be a simplified diagram that shows the design strategy for the ligation (e.g., some of what is shown in the 'Roadmap for Plasmid Construction' figure that appears on the wiki for Day 1). However you should not copy and paste this figure from the wiki into your report since it emphasizes the days of the module more than the construction of the expression plasmid.
 * Figure 3: Your gel showing your PCR results. Keep in mind that all images of gels must include markers indicating the estimated sizes of the observed fragments (these can be estimated by eye based by comparing to the markers). You will certainly need labels indicating the sizes of two or three fragments in the ladder.
 * Figure 4: The gel showing the purified products. See above comments on for Fig. 3  regarding correct labeling.
 * Table 1: Data showing your transformation results, including data for the transformation controls and the calculated transformation efficiency (in the table legend or key if you like).
 * Figure 5: Diagrams showing rough plasmid maps to explain the logic of how you know whether or not you obtained the desired vector. You should indicate the positions of the restriction sites that you used for your analysis, and indicate the sizes that you expect for digestion. Ideally you would also indicate the position of the coding sequences. You will need diagrams of the parental backbone and the correct product.  Please explain to the reader how you know that you do not have multiple inserts (if you indeed know this to be the case).
 * The restriction site positions need not be perfect to the base pair, but should be correct within ~50 bp (e.g., the reader need not know the fragment is 2.543 kb – it is sufficient to state that the fragment is 2.5 kb).
 * Figure 6: The gel showing the results of your restriction analysis. See above comments on for Fig. 3 regarding correct labeling.