Laboratory Procedures

The heart of the ModBio class is the laboratory project that we work on throughout the semester.  The project that we do reinforces key concepts that students read about and discuss in class.

We spend the first two weeks learning about lab safety, finding where things are, forming teams and practicing some essential laboratory skills. Some of the important information that we share with students is below. The techniques that we perform during the first two weeks can be found on the “Getting to Know the Lab” page.

The lab procedures are listed in the order in which we perform them, and together they make a semester-long  project that involves cell culture, microbiology, biochemistry and molecular biology techniques.  Students develop a deep understanding of the concepts and tools used to study gene regulation and cell growth.  However, it is not necessary to complete the entire sequence of activities to gain valuable laboratory experience.  Many of the techniques can have short cuts in which resources are prepared or purchased ahead of time.

General Lab Tips

  1. Keep your lab notebooks current.
  2. Read ahead in the lab manual, both prior to the upcoming lab and during the lab itself.
  3. Collaboration is encouraged! Real biologists collaborate extensively.

You will be working in teams of 2 or 3; however it is acceptable and encouraged to interact with other groups.

Laboratory Advice

  • Always clearly label tubes, plates, flasks, etc.
  • Mix reagents appropriately: vortex, pipet and stir as directed (ask if you are unsure).
  • Sometimes one person’s error is another person’s data.
  • Don’t blindly trust machine readings (spectrophotometer, luminometer, etc.), if they seem way “off”. Double check by another means if possible. Take a second reading if your numbers are peculiar.
  • Remember your ‘controls’ (positive and negative) and what they indicate.
  • Measure volumes carefully, with the correct size pipettes.
  • Tape or staple your gel images into your notebooks, in the ‘top to bottom’ orientation.
  • Write it down, even if you think you can remember it.
  • Double-check protocols to see that they reflect what will actually be done in the lab. (Sometimes there are minor changes, which the instructors will point out.)
  • Be courteous in lab- don’t steal/borrow things from others without permission.
  • Don’t leave the lab without making sure that everything is written down in your lab notebook.
  • Don’t leave the lab without making sure that your prepared sample(s) are properly put away for safe storage!

Keeping a lab notebook

Each team maintains a single lab notebook, which is a hand-written, dated log of your laboratory activities as they are performed. This is the notebook that will be assessed periodically by your instructors and TAs, resulting in a “team” grade, shared by each team member, that will count towards your final lab grade. In addition, we encourage each individual student to maintain notebooks for their own records, although their maintenance and upkeep will be left to the discretion of the student. The “team” lab notebook will contribute 10% toward your final grade.

You must use a traditional type of lab notebook (not a composition notebook used for writing stories). In our view, a hand-written lab notebook that is properly maintained represents the most ‘tamper-resistant’ chronicle of lab activities.

Beginning with the week that the cloning project commences, the maintenance of the team notebook is to be performed on a rotating basis by each team member. For example, during week one, entries in the notebook for that series of procedures will be documented as described below by one team member, who will sign and date the notebook at the end of his/her section (in addition to the dates at the top of each page). The following week, the maintenance of the notebook will be the responsibility of the next team member, and so on.

How to organize a lab notebook.

  1. Date, title, rationale: Every page needs to have a date written (on top, preferably, can be on the left or right side). Write out the title of the experiment near the top of the page, followed by a brief rationale/objective (in your own words) for the day’s activities. In brief, what are you setting out to accomplish, and why? On subsequent pages documenting the same experiment, include the date and at least an abbreviated title (eg. “Transformation, cont.”). Make sure that you number each page, if they aren’t numbered in the book already.
  2. Protocol: In this section, make reference to the numbered protocol in the weekly document that you will receive; identify it by name and any other indicators available. As necessary, make note of any divergence from the original posted protocol, no matter how trivial it may seem to you initially (whether accidental or deliberate). Write down observations, questions, anything that seems relevant as you are performing the protocol. Drawings/sketches may be used to depict what you are doing.
  3. Results: This section is for all your results, in whatever format they happen to be in; written observations, drawings, tables, charts, graphs, etc. Tape (or staple) all data printouts (e.g. pictures and luminometer readings) immediately into your lab notebook in the appropriate spot. Label and date your pictures directly so that it isn’t necessary to refer back a few pages in your notebook to figure out what the photo represents.
  4. Interpretation (as appropriate): Comment on results, while everything is fresh in your mind. State the obvious, but also try to see if there is any additional info that you can extract from the results.

For ex., rather than write, “it worked”, write that you ..’saw DNA bands of the appropriate size for supercoiled plasmid DNA, and that there also appeared to be another band that may represent a different form of DNA’… Speculate on what it might be.

Make a note of any errors that were made during the procedures and any steps that were taken to correct the errors. These notes can be written in at the appropriate sections of the protocol, provided clarity is maintained.

Similarly, make a list of any questions you have about the procedures, at any appropriate section.

Questions: In most cases, we will prepare a few questions for you to answer in your notebooks, on aspects of each week’s procedures. These will be designed to help you to think through what you are doing, and to demonstrate your understanding of the procedures. Even if you are not sure of the answers, write down something that represents your best current understanding. These can (and should) be a collaborative effort of all team members, regardless of who is ‘in charge’ of the current week’s write-up!

ACKNOWLEDGEMENTS:

All lab procedures and tips were created in collaboration with Sadie Aznavoorian-Cheshire, Ph.D.  Each class of Modern Biology has made contributions to the laboratory portion of the course with helpful suggestions and ideas for improvement of experimental procedures and the written manual. Special mention goes to the inaugural class of Modern Biology for tirelessly testing protocols, reagents, equipment and schedules, and to the Modern Biology class of Fall ’09 for helping us to brainstorm ideas for modification of the initial cloning project. The list of people to thank and acknowledge has now grown very long over the years, and any written list would almost certainly be incomplete. Rather than providing a long list, then, we would like to collectively thank and give special recognition to every former Olin Biology student who has played a role in making the laboratory experience a better one. The students’ perspective is very important as we seek to develop the projects that provide the optimum learning experience, and for us this is an on-going process.

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