20.109(S08):Wrap-up analysis (Day7)

Introduction

Today we’ll complete the final piece of analysis for module 3, namely quantifying the collagen protein content in samples cultured under different conditions. As with other analysis in this module, the results will be presented informally in your notebook rather than in a more formal assessment.

You should spend the remainder of your time today preparing for your research proposal presentation, first by discussing the general idea and technical content with one of your peers, then by working on the actual construction of your slides and getting some feedback on them from the teaching faculty.

Protocols

Part 1: ELISA analysis

The analysis of protein concentration that you perform today will be similar to the titration curve analysis that you did in Module 2.

1. Open the text file containing your raw data in Excel, and save it as an Excel file.
2. Label the columns to reflect your samples. It may be easiest to visually separate samples (in the first few rows of the sheet) and standards (in the next few rows), since they will undergo partly different manipulations. You may also want to work on two separate worksheets, one for each collagen type.
3. Average your replicate values for both standards and experimental samples.
4. Now calculate the average of your blank samples, then subtract this background value from each of your raw averages. (So far your column headings might look like: REP1, REP2, AVE, AVE-SUB.)
5. You will use your standard readings to make a calibration curve. Plot the absorbance readings for the standards (on the x-axis) vs. the known concentration of collagen added (on the y-axis). Just type in the first concentration, and divide by two down the column.
6. Click in the chart area, then choose menu Chart → Add Trendline. Click on the Options Tab, and choose to display both the equation and the R² value on the chart.
7. Delete data points that seem to be outside the linear range of the assay (just delete the AVE-SUB value, not the raw data!), until you get a reasonable R² value for your line, i.e., one that is close to 1. The equation should update in real-time as you delete data.
8. Now that you have the slope and intercept of the line, you can feed this information back into the absorbance values for your experimental samples, and calculate the actual protein concentrations. If you are unsure of how to proceed, ask your peers or instructors. The $ symbol in Excel is useful here for efficient calculations, in case you want to compare the results for multiple slope/intercept values.
9. Your results will most likely be closer to ng/mL than μg/mL, so go ahead and convert them.
10. Finally, address the following in your notebook (and update your results summary on the Day 6 talk page):
    • which samples had a measurable amount of collagen I? collagen II?
    • for samples with both values in range of the assay, what was the collagen II:I ratio?
    • how do these results compare to those at the transcript level? what factors might cause any differences that you see?

Part 2: Cross-group research idea discussion

You should be on your way to becoming an expert on your research topic. You should have been reading and thinking a lot about it and you may feel
(a) like there's too much to read
(b) like you have too many ideas and no way to map or prioritize them
(c) like you don't understand what you're reading
(d) all of the above.

One of the best ways to help frame the problem for yourself is to discuss it with someone new. Take some time today to talk with someone from another lab group. That group will offer you a fresh ear to consider your proposal. Try to describe your research problem to them. Articulate why it's important. Tell them about some recent, relevant data. Describe what you're proposing to do and what the findings from your experiments might reveal. Throughout your discussion, keep careful track of the questions they ask since these will point you to the confusing concepts or fuzzy parts of your explanation or understanding.

Then be a good listener to hear the proposal that they've been working on. Ask lots of questions. No questions are dumb. You are there to offer a naive ear and seek complete explanations. You will have time at the very end of class to reconvene with your own lab partner to hear how their conversation went. Try to identify repeated questions or concerns since these are probably the holes in the project as it stands. You can rework your proposal based on the conversations you've had.

Part 3: Prepare for presentation

Next time you will present your research proposals to the rest of the class. Try drafting at least 2 or 3 slides if you can. Atissa will come by to critique your slides and answer questions ~ 4 pm.

For next time

Prepare a 12 minute powerpoint talk that describes the research question you have identified, how you propose to study the question and what you hope to learn. More detailed descriptions of the elements of the oral presentation can be found in the FNT assignments and the protocols associate with this Module as well as with the research proposal guidelines. When it is ready, please email your presentation to astachow AT mit DOT edu. Speaking order will be determined by the order that presentations are received.

On the day you present (see announcements on front page for when and where) your team should print out and bring two copies of your powerpoint slides. Black and white is fine and you can print more than one slide per page if you like (4-6 slides per page tends to be ideal for my note-taking). You should also write (and print out) your "talking points" in the comments box of each slide. These are speaking notes for your presentation, and should include short phrases to remind you of the key points to cover on each slide, as well as the transitions you've planned between them. For example, in last year's presentations one slide's talking points were:

As you can see from this image, taken from a review on hydrocarbon metabolism in marine bacteria, the alcanivorax species is the first to grow in population after an oil spill, and its growth correlates with a decrease in aliphatic hydrcarbons.

• After most alkanes have been degraded, the Cycloclaticus species blooms while aromatic hydrocarbon levels decrease
• One thing to note is that as soon as they have done their job, both species return to their normal population levels.
• One problem with using Alcanivorax and Cycloclasticus to clean oil spills, however is that they can only be found in specific locations

The next slide (transition statement) began: To remedy this, we decided to look into other bacteria into which we could move the hydrocarbon metabolic pathways

You don't have to use complete sentences in your own talking points, but the above example should give you a sense of what content is expected.

You will be graded on the integrated success of your presentation: concepts, slides, talking points, and presentation.