Lab 2: MINI LAB REPORT
Refer to the general guidelines for Mini Lab Reports on Canvas, found here (link opens in a new tab): Mini Lab Report Guidelines
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:
- What is the protein you are working on and why is it interesting to the general public?
- Provide relevant molecular details about HCAII, and include a helpful PyMOL figure of the protein.
- What is the hypothesis or question you are addressing with this project? For this week, choose any mutation you want. Write a detailed, biochemical hypothesis for that specific mutation. The objective is to practice the process of developing a hypothesis; you will work later in the semester to write a hypothesis specific to the mutation you will actually be studying.
- 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.
- Throughout your introduction, use 2-3 literature sources. Be sure to use in-text citations and include a reference section at the end of your report (scroll to the bottom of Mini Lab Reports for more on references).
A Note on Nomenclature
When referring to a gene, its name should be italicized (HCAII), but when referring to a protein, its name should not be italicized (HCAII). Also, some of you may be used to studying bacterial genes, whose names are typically written using lowercase letters. Mammalian genes, by contrast, are written using capitol letters.
Methods
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.
For this report, be sure to include:
- A statement on the purpose of the experiment (“In order to amplify the HCAII gene and pETblue2 vector, …)
- 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
- The %agarose and final concentration of EtBr used in the gel
- How the gel was visualized
Do NOT include:
- Details like “tubes were labeled” or “agarose solution was microwaved.” These are standard procedural steps that any scientist would know to do.
Results
You can download the gel image you will use in this section here: Lab 3 Agarose Gel
Start the Results section with a sentence to remind the reader of the overall goal and/or hypothesis for the experiments you are describing – something similar to the purpose statement mentioned above for the Methods section.
Be sure to include:
- A figure of the gel containing the PCR products. Highlight the expected products with an arrow or box. 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
- 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
- If you observe any unexpected bands, comment on their existence and their apparent size. This is not a Discussion section, so you do not need to discuss what they might be.