Instructions for the first Lab Report: the effect of  lysozyme.

Authorship
Even if you worked together on the experiment, and even if you worked together on the report, each person must turn in their own, unique report, written in your own words.
DO NOT: pass in a report that looks substantially like someone else's.
DO NOT: pass in a report that uses sentences from your handout.
DO NOT: pass in a report that contains text lifted from a textbook or the internet.

Working with Data
This is not a software course, so you're not expected to learn Excel entirely on your own. Do not wait to get help.  Software help is FREE! I will answer any question I possibly can, whether by phone, email, or in person. Your TA can also help.
The data is available at this link:  Lysozyme-Excel and is copied at the end of this page.
The morning class used both Shigella flexneri (A-D) and  Pseudomonas aeruginosa  (E-H) and the afternoon class used Micrococcus luteus (which is also called M. lysodeikticus) (Q-V) . The results from Gram negative organisms have not been very good the last few years, but we will use the data obtained with Pseudomonas in the report. So, ONLY  Trials E-H from the morning will be used and All of the afternoon data (Q-V) will be used (by everyone in BOTH sections).
        You will notice that the starting OD readings vary among the different samples. This makes it difficult to compare results. For this reason, you will need to convert the data to "Fraction of Initial OD". Another way of saying this is that, for a particular trial, you will compare all the OD readings for that trial to the starting OD reading (at T = 0). For each sample, divide each value by the OD reading at time = 0 for that sample. This gives you a decimal fraction where 1.00 is no change, 0.50 is half as much, etc. Two decimal places will give data that are easily compared and won't exceed the allowable number of significant figures. This calculation is actually very easy in Excel, and there is a link to some tips about making Excel work for you below.
It is very important that you understand the different options in the Excel graph menu. Not all graphs are appropriate for all kinds of data. Because the readings vary continuously over time, you must use an x-y scatter plot, and you may allow Excel to smoothly connect the points if you wish.  In deciding how many graphs you want to make and what data to combine a graph, consider the following things:  Which trials are you comparing? Does it make sense to show a set of data without its control? What helps you to see differences in the different trials? If the graphs are too cluttered, they will be hard to see. If you don't put enough data on a graph, how can you compare anything?  Finally, can you visually compare the changes in samples if the graph axes are different?

You may want to review pages 5-8 in your lab manual, especially the pages on experimental design and controls.  This will help you to understand why we did all the different "trials" that we did.

Report structure

Each lab report should have 4 sections: an Introduction, a Methods or Procedures, a Results (any graphs and brief description of them), and a Discussion. Actual headings are strongly recommended. No Literature Cited or Reference section is needed nor do you need an Abstract.  Lab Reports for this class do not need to be as formal as a journal article.

Introduction:   This experiment is about the importance of peptidoglycan and the Gram negative outer membrane. In your introduction you should say what peptidoglycan does for the cell, what lysozyme does TO the cell, and how Gram negative cells are protected from lysozyme. Say something about why the experiment was done. It may help you focus your thoughts to put forth a hypothesis that you think was tested in this experiment. You are required to use your own words as much as possible. Think of this more as a short essay which provides background information for understanding the experiment.

Methods:  Briefly explain the procedure that you used.  How did you determine if anything was happening to the cells? Be sure all descriptions of the procedures are written in PAST TENSE. You are not writing an instruction manual, rather, you are giving an account of what you did. Do not fill this section with pointless little instructions on how to use the equipment.

Results: What "transformation" did you do to the data to make it easier to work with (see instructions above)? Graph the transformed data on the Y axis, and time on the x axis.  Group samples together in your graphs in a way that makes sense; I figure you need at least 2 graphs for legibility sake, maybe more, maybe not. 

Conclusions: Your Conclusion is essentially an essay that explains what should have happened and why and especially what did happen and why. Rely heavily on your data. Don't draw conclusions that aren't supported by your data. As a guide to drawing conclusions from these experiments, you should answer the following questions in your write-up, but do not separately list the questions, just weave the answers together when saying what happened. First, results for the Gram negative bacterium: Did the lysozyme alone lyse the cells? Why or why not? Did the EDTA have any effect, and what kind of effect was expected?  For the Gram positive: Did the lysozyme lyse the cells? Why were the other solutions added and what result was expected?  Finally, compare the results for the Gram negative and Gram positive in samples where only lysozyme was added; what difference was seen and why? Which trials functioned as controls?

This report is due Wednesday, September 17 by 6 pm.

Special note on working with Excel:
As many of you know by now, I usually answer questions with more questions, trying to get you to do the work of figuring things out. However, this is not a software class. HELP USING EXCEL IS FREE!!! PLEASE ASK ABOUT ANYTHING YOU'RE HAVING TROUBLE WITH, AND I WILL GIVE YOU ADVICE. Don't do all the work on your calculator and enter it into Excel only to make the graph! You will waste too much time.  Please click HERE for some important suggestions.

Here are the raw data. The left column is time in minutes. The remaining columns are Optical Density at 546 nm. You are analyzing all the data.