Required Format of Report:

RATIONALE: Describe the thinking and principles behind your approach. This is not a description of experiments you will do. It is the logic that will enable anybody to understand why you choose those experiments.
For example, the rationale for cooking pizza is 'by preparing a scrumptious, heat-killed, carbohydrate and protein rich morsel, I can satisfy my neurological craving and nourish my body'. This is different from 'take some flour, tomato paste, etc.'
Until you have told me the why in the rationale, I'll be damned if I'm going to collect flour, tomatoes, etc. Hence, rationale precedes instructions and is a vital part of the game.

EXPERIMENT(S) and RESULT(S): Briefly but exactly describe the key experiments and the results such that somebody else can repeat it (i.e., 'Plating a 1 in 10^4 dilution of Phage #1 on E. coli B gave me 12 small plaques'). Key experiments are those from which you will derive your conclusion - don't tell me everything you did, tell me only what I need to know to assess your conclusions. Most importantly, describe appropriate controls for your experiment.
For example:
- Plated phages 1 & 2 using 1:10 dilution with E. coli K, no progeny after multiple attempts.
- Plated phages 1 & 2 using 1:2 dilution with E. coli K, 2 progeny found, placed in fridge, slot 4 and 5.
Controls:
- Plated only phage 1 using a 1:10 dilution ratio on E. coli K, no progeny
- Plated only phage 1 using a 1:2 dilution ratio on E. coli K, 3 progeny placed in slots 5, 6, 7.

NOTE that the control differs only in one respect from the experiment, the kind of phages used, all other conditions (dilution, E coli strain, etc.) are the same!

CONCLUSION: Describe the conclusion you have derived from the experimental results that you have you listed in the results section and which need to summarize here. Importantly, tell us why you come up with this particular conclusion.
Example: "I conclude that phage #1 and phage 2 are xxxxx because wild type phage grows on E, coli K."

Example Report: (partial write-up for phase I of problem #2)

Problem 2: Identify phage with compensating mutations

Rationale: Since the starting phage is a frameshift mutant, it will not form plaques on E. coli K. If I plate out large numbers of phage on K and observe viable plaques, these must either be: 1) contaminants, or 2) mutant derivatives of the parent that have undergone a genetic change that allows them to grow (revertants). Since the former don't occur in the simulation, the new phages must be double mutants that aquired a second mutation that is able to suppress the effects of the first mutation. This will be confirmed (control) by plating on E. coli B, which should result in small but not large plaques.

Observations:
- Plated a 1:10 dilution of phage #1 (the starting mutant) onto E. coli K. I observed 5 small plaques growing, and harvested these to the 'fridge (1-5).
In comparison (control), plating the same amount of phage on E. coli B results in complete lysis.
- To confirm the properties of phages 1-5 (being revertants), I plated each of them on E. coli B at a dilution of 1 in 10^4 and observed ~50 small plaques indicative of wild type phenotype.

Conclusions: The phages 1-5 in my fridge are most likely revertants containing the original mutation and a new mutations of the opposite because the phages grow (form plaques) on E coli K and form small plaques on E. coli B.
While it is possible that one or more of them are true revertants (original mutation restored to wild type sequence) this is unlikely since there are many, many different ways to restore the reading frame (i.e. any nearby -1 deletion should restore a +1 frameshift), whereas there is only a single change that will restore wild type sequence. For similar reasons, it is unlikely that any of the phage contain identical second mutations.

On Writing up your results and the Granting Process:
Remember, to unlock a 'red' scenario, you need to BRIEFLY tell me or a T.A. your concept for solving the problem and the experimental approach you will take. You can do this 'live' or in by an e-mail.
To write up your report use any text software (word, word perfect, etc) and submit your report in the "Dropbox" of the D2L website of the course using the following file formats: microsoft word document (report.doc), rich text format (report.rtf), or Acrobat pdf format (report.pdf). To log in use your UA-net-ID and open link to MCB422 in "academic courses" window.