LABS 2&3 MINI REPORT

Refer to the general guidelines for Mini Lab Reports on Canvas, found here (link opens in a new tab): Lab Mini Reports

Introduction (draft 1)

This week, you will write a first draft of the Introduction section for your final lab report. As such, think of this as an introduction to the entire 551 HCAII project; not an introduction to doing PCR.

The introduction will provide the context for your lab report by summarizing what is currently known about your topic and stating the hypotheses or questions you are studying. The introduction should briefly describe the rationale of the work and the approach you took. Use the active voice. When presenting published information, use the present tense (i.e. this is what we currently know). Introductions start out with a description of the general background about the problem and focus down to the specific question you are studying.

Your introduction should be 1-2 double-spaced pages long.

Your introduction should address the following:

1. What is the protein you are working on and why is it interesting? Use 2-3 literature sources for this section. Be sure to use in-text citations and include a reference section at the end of your report (scroll to the bottom of Lab Mini Reports for more on references).
2. Include a helpful PyMOL figure of HCAII.
3. What is the hypothesis or question you are addressing with this project? For this week, choose any one of the six mutations that the class will be studying this semester (see mutant list below). Write a detailed, biochemical hypothesis for that specific mutation.
4. Give a general description of the experiments you will use to address your question/hypothesis. Since you’ve only done one lab experiment thus far, don’t worry too much about this yet; just look forward in the lab manual and write a sentence or two on what we will be doing this semester.

Mutation List:

Y7F

H94W

H96F

L198K

T199C

T199S

Methods

You are only reporting on lab 3 procedure and Part 3 of the lab 2 procedure, i.e. the PCR. Do not report anything from the pipette practice and primer design exercises.

It is difficult to include the right amount of detail in a Methods section. Remember that the goal is to provide enough detail that someone with a scientific background could repeat your experiment. You do not need to write out detailed protocols.

For your first few mini lab reports, we will tell you exactly which details to include. Gradually, you will be expected to include appropriate information more independently.

Be sure to include:

• Purpose statement/brief summary of the experiment (“In order to amplify the HCAII gene, …)
• Cite the lab manual
• Components added to the reactions: for most components, report the final concentrations. DNA and Phusion should be reported as the total amount per reaction (in nanograms and units, respectively).
• Sequences of the primers you used, pointing out which sequences are vector vs. insert
• A description of the negative control
• How you visualized the DNA
• Enzyme used for digestion
• How you purified the DNA (you DO NOT need to include the full protocol for DNA purification – simply state that the DNA was purified using a spin column)
• How you measured the DNA concentration

Do NOT include:

• Details like “tubes were labeled” or “aliquots were kept on ice.” These are standard lab procedures that scientists would know to do.

If you are not sure how to write the methods section, you may use the methods section of published papers as a reference. You can do this for other sections as well.

Results

Be sure to include:

• Figure: gel of the PCRs. Highlight bands of interest with an arrow. Label each lane and all of the size markers (for more information on the ladder: NEB quick load DNA ladder ). Your figure legend should include:
  • A figure number and short title, bolded
  • The % agarose
  • What is in each lane
  • What your box/arrow is highlighting
  • DO NOT interpret the gel in the figure legend

View the following video for tips on making a great gel figure:

• If you did not get any PCR products, you should still show and label your gel

• Text description of the PCR products:
  • Which reaction(s) yielded product
  • The apparent size of the product and whether that matches the expected size
  • Whether some reactions yielded more product than others
  • Any other observations you have about the appearance of the product
  • The concentration and purity of the purified PCR products

• The concentrations and purity of DNA in a table format (note that, like figures, table should have a legend; however, table legends go above the table. Similarly, like figures, you need to explain your table in the Results section).

Here is a brief writing workshop on the Methods and Results sections.